Methods for Terpenoid Production

ABSTRACT

A bacterial strain comprising one or more vectors encoding a) one or more enzymes to produce one or more terpene precursors; and b) a fungal terpene synthase (FTPS). The present invention also relates to a method of producing a terpenoid comprising a) culturing the bacterial strain described herein in an expression medium; and b) isolating the terpenoid from said expression medium.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority of Singapore application No. 10201807514P, filed 31 Aug. 2018, the contents of it being hereby incorporated by reference in its entirety for all purposes.

FIELD OF THE INVENTION

The invention is in the field of biotechnology. In particular, the invention relates to methods for the discovery of fungal terpene synthases and the use of fungal terpene synthases for the production of terpenoids.

BACKGROUND OF THE INVENTION

Terpenoids constitute one of the most structurally diverse classes of natural products with wide applications as pharmaceuticals (such as Taxol and artemisinin), as food coloring (such as carotenoids), flavors and fragrances (such as nootkatone and sclareol) and biofuels (such as farnesene). The terpenoid diversity is attributed primarily to terpene synthases (TPSs), which convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic terpene scaffolds. Specifically, the terpene skeletal diversity arises from two main features of TPSs: a large number of TPSs with vastly different functions and the ability of many TPSs to catalyze multiple terpene products from a single substrate. Almost half of the characterized monoterpene and sesquiterpene synthases produce significant amounts of additional products, apart from their main products.

Structurally, all sesquiterpene synthases (STSs) from plants, fungi and bacteria have a conserved metal binding motif (unlike plant STSs are DDXXD, fungal STSs are DE(N)XXD) and NSE triad. However, outside of the motif, there is limited sequence similarity between plant and microbial TPSs. Many plant TPSs have been discovered and studied over the past few decades, however, the study of fungal terpene synthases was lagging behind. Currently, only a handful of fungal TPS have been cloned and functionally characterized (less than 50, Table 1).

Fungi have enormous diversity (-5 million species) and outnumber plants by at least 10 times. Each fungus has an average of 10-20 putative TPS homologs in Basidiomycota, indicating that fungal terpenoids and TPS genes represent rich but largely untapped natural resources. In addition to the discovery of novel TPS genes and terpenoids, it is also valuable to identify other potentially more efficient TPSs than existing TPSs with the same functions or products. This is due to the various applications of terpenoids and huge commercial interests in terpenoids. In some cases, the production of terpenoids was limited by insufficient activity of terpene synthases. Identification of TPS enzymes with novel products, superior activity and selectivity would greatly benefit the industrial biotechnology society for terpenoid production.

SUMMARY

In one aspect, there is provided a bacterial strain comprising one or more vectors encoding

a) one or more enzymes to produce one or more terpene precursors; and

b) a fungal terpene synthase (FTPS).

In another aspect, there is provided a genetically modified 1-deoxyxylulose-5-phosphate synthase (DXS) enzyme, wherein the genetic modification is a mutation at one or more amino acid positions.

In another aspect, there is provided a genetically modified fungal terpene synthase (FTPS), wherein the genetic modification is a mutation at one or more amino acid positions.

In another aspect, there is provided a method of producing a terpenoid comprising a) culturing the bacterial strain as described herein in an expression medium, and b) isolating the terpenoid from said expression medium.

In another aspect, there is provided a method of producing a terpenoid comprising a) culturing a bacterial strain comprising a vector encoding the genetically modified FTPS as described herein in an expression medium and b) isolating the terpenoid from said expression medium.

In another aspect, there is provided a fungal terpene synthase (FTPS) encoded by a polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO:39.

In another aspect, there is provided an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO:39.

DEFINITIONS

As used herein, the term “terpene” refers to a class of organic compounds produced by plants, bacteria, fungi and insects. The building blocks of terpenes have a five-carbon isoprene unit.

As used herein, the term “terpenoid” refers to a large and diverse class of organic compounds derived from terpenes and include terpenes. The building blocks of terpenes have a five-carbon isoprene unit and contain additional functional groups, typically oxygen-containing functional groups. Terpenes are a subset of terpenoids.

As used herein, the term “terpene precursor” refers to a substrate that is converted to a terpene or terpenoid by a terpene synthase. The substrate may be converted to a terpene or a terpenoid.

As used herein, the term “terpene synthase” (TPS) refers to an enzyme that converts terpene precursors to terpenes and/or terpenoids. The term “fungal terpene synthase” (FTPS) refers to a terpene synthase that is isolated from a fungus.

As used herein, the term “UP” in the context of a fungal terpene synthase (FTPS) refers to a domain of the FTPS. The UP domain is situated upstream of the DW domain.

As used herein, the term “DW” in the context of a FTPS refers to a domain of the FTPS. The DW domain is situated downstream of the UP domain.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention will be better understood with reference to the detailed description when considered in conjunction with the non-limiting examples and the accompanying drawings, in which:

FIG. 1 shows the volatile terpenoids produced by A. aegerita. Volatile metabolites from A. aegerita culture were sampled by solid phase microextraction (SPME) and analyzed by GC-MS. The structure and mass spectra of identified terpene compounds are shown in FIGS. 4 and 5, respectively.

FIG. 2 shows experimental results for the improvement of the solubility and activity of DXS enzyme. In all measurements, S0 is the wide type DXS from Escherichia coli. (A) shows the solubility and soluble DXS at 5 h after induction. (B) shows the in vitro enzymatic activity measurements of DXS and its mutants. (C) shows the specific lycopene yield when different DXS mutants were used. (D) shows the annotations for DXS mutants.

FIG. 3 shows a schematic of an engineered Escherichia coli strain for screening of terpene synthases. Metabolites in the pathway are: GAP, glyceraldehyde-3-phosphate; DXP, 1-deoxy-D-xylulose-5-phosphate; MEP, methylerythritol phosphate; CDP-ME, 4-diphosphocytidyl-2-C-methyl-D-erythritol; CDPMEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol-2-phosphate; MEC, 2-C-methyl-D-erythritol-2,4-diphosphate; HMBPP, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl pyrophosphate; GPP, geranyl pyrophosphate; FPP, farnesyl pyrophosphate and GGPP, geranylgeranyl pyrophosphate. Enzymes are: dxs, DXP synthase; dxr, DXP reductase; ispD, CDPME synthase; ispE, CDPME kinase; ispF, CDPMEP synthase; ispG, MBPP synthase; ispH, HMBPP reductase; idi, IPP isomerase; STS, sesquiterpene synthase and MTS, monoterpene synthase.

FIG. 4 shows the terpene compounds identified in this study.

FIG. 5 shows the mass spectra of terpene compounds analyzed in this study.

FIG. 6 shows the predicted biosynthetic gene clusters in A. aegerita. Four putative TPSs (AAE3_09008, AAE3_06743, AAE3_04444 and AAE3_05024) compile to an own cluster. Four of the STS genes (AAE3_10454, AAE3_12839, AAE3_04120 and AAE3_13291) are part of clusters consists amongst other of two to five P450 monooxygenases.

FIG. 7 shows the terpenes produced by E. coli expressing TPS genes from A. aegerita. The metabolites were analysed by GC-MS with DB5 column. The metabolite profiles analysed by GC-MS with VF-WAXms column were shown in FIG. 8. Major compound peaks are labelled by numbers corresponding to structure shown below. See FIG. 5 for mass spectra and Table 3 for summary of terpene compounds analysed by both DB5 and VF-WAXms column.

FIG. 8 shows the GC-MS profiles of terpenes produced by E. coli expressing TPS genes from A. aegerita. The metabolites were analyzed by VF-WAXms column. ‘Ctrl’ is the GC-MS profile of volatile metabolites produced by E. coli strain with empty vector. Indole (*) endogenously produced by E. coli serves as an internal reference to compare the relative amount of the terpene production.

FIG. 9 shows the nuclear magnetic resonance (NMR) spectroscopy analysis of the product of AAE3_10454.

FIG. 10 shows the use of essential oils as chemical standards to identify terpene compounds identified. VF-WAXms column was used in this study.

FIG. 11 shows the use of essential oils as chemical standards to identify terpene compounds identified. DB-5ms column was used in this study.

FIG. 12 shows the GC-MS profile of monoterpenes produced by AAE3_9164.

FIG. 13 shows the phylogenetics of characterized TPS homologues from four fungi. TPSs from A. aegerita (AAE3), C. cinereus (Cop), O. olearius (Omp), Stereum hirsutum (Stehi1) and the single TPS described from Armillaria gallica (Pro1). Sequences used in the final alignment can be found in Table 1. The TPSs highlighted with a square (“▪”) had no detected terpene products.

FIG. 14 shows the comparison of different GC columns for the analysis of terpenes. Niaouli essential oil was used as standards of viridiflorene 6 and viridiflorol 7. Viridiflorol 7 has relatively lower signal than viridiflorene 6 in DB-5 column as confirmed by authentic chemical standards from Santa Cruz Biotechnology (FIG. 17). The difference of relative intensity of viridiflorol and caryophyllene (structurally similar to viridiflorene) in DB-5 and VF-WAXms were further verified by authentic standards.

FIG. 15 shows the similarity analysis of AAE3_12839 (SEQ ID NO: 34) and TPS31 (SEQ ID NO: 75) from Solanum lycopersicum (Tomato). The fungal viridiflorene synthase (AAE3_12839) shares little identity and similarity with plant viridiflorene synthase.

FIG. 16 shows the similarity analysis of AAE3_13291 (SEQ ID NO: 32) and MqTPS1 (SEQ ID NO: 76) from Melaleuca quinquenervia. The fungal viridiflorol synthase (AAE3_12839) shares little identity and similarity with plant viridiflorol synthase.

FIG. 17 shows the proposed reaction mechanisms for the formation of major products. The carbocation from FPP ionization undergoes two different primary ring closures (1,10 or 1,11 closure). Major compounds produced by recombinant A. aegerita TPSs are labelled by numbers, including Δ6-protolilludene 1, y-muurolene 2, β-cadinene 3, δ-cadinene 4, α-muurolene 5, viridiflorene 6, viridiflorol 7, δ-cadinol 8 and epicubenol 10. See FIG. 5 for the mass spectra.

FIG. 18 shows the phylogenetic tree of TPS homologs identified in 85 Basidiomycota and 239 Ascomycota genomes. (A) shows all the fungal TPSs clustered into seven distinct clades. The characterized TPSs in this study and in literature were labelled in the figure. See more information in Table 1. In particular, these include A. aegerita (AAE3), C. cinereus (Cop), O. olearius (Omp), Stereum hirsutum (Stehi1), Hypoxylon sp (Hyp), Fusarium fujikuroi (Ffsc4, Ffsc6, STC3 and STC5) and a few aristolochene synthases (AtARS and PrARS). Most of Basidiomycota TPSs (including all the 11 A. aegerita TPSs) clustered in clade I, II and III, but Ascomycota TPSs scattered in clade IV, V, VI and VII. (B) shows potential Δ6-protoilludene synthases based on the phylogenetic analysis. The TPSs highlighted with a circle (“●”) were characterized in this study or in literature.

FIG. 19 shows a bioinformatics-guided predictive framework—all-by-all BLAST. The All-by-all BLAST of the 1408 putative TPS candidates was performed with enzyme function initiative (EFI)—enzyme similarity tool (EST). Sequence similarity networks (SSN) were generated by filtering the sequences into clusters at the alignment score of 100. SSNs were used for visualization by Cytoscape version 3.5.1. The model obtained here was used together with the phylogenetic tree in FIG. 13 to predict the TPS functions based on the sequence similarity and characterized TPS in this study and in literature.

FIG. 20 shows a predictive example of the clustering of putative fungal linalool/nerolidol synthases (LNS). Based on EFI-EST analysis, a group of TPS homologues were clustered with AAE3_9435. By setting the alignment score to between 80 and 90, a smaller set of candidates were selected.

FIG. 21 shows a predictive example of the validation of putative fungal linalool/nerolidol synthases. Selected putative LNSs were expressed in the engineered E. coli strains. LNSs chosen here in the cluster are from Agrocybe aegerita (AAE3), Agrocybe pediades (Agrped1), Galerina marginata (Galma), Hypholoma sublateritium (Hypsu1), Hebeloma cylindrosporum (M413). Agrped1_689675 is found to a novel monoterpene synthase, linalool synthase (LS), while the others are bifunctional LNSs.

FIG. 22 shows the Sequencing alignment of validated LNSs and the LS. Sequencing alignment indicated similar positions of these TPSs are 107/34=31%. Based on the alignment, a key amino acid F204 was identified that could impact the activity of the LS (Agrped1_689675).

FIG. 23 shows the results of the engineering of the LS Agrped1_689675. The three mutants (F204D, F204G and F204R) have different product profiles to that of the wildtype enzyme. It produced both geranyl acetate (predicted by National Institute of Standards and Technology (NIST) library) and linalool. The other mutants (F204I, F204L and F204V) share the same product (linalool) with the wildtype Agrped1_689675.

FIG. 24 shows a predictive example of the clustering and validation of putative fungal viridiflorol synthases. According to the phylogenetic tree in FIGS. 18 and 19, 15 fungal TPS homologs were closely clustered. Four of them (Sphst_47084 from Sphaerobolus stellatus, Denbi1_816208 from Dendrothele bispora, Galma_104215 from Galerina marginata and Pilcr_825684 from Piloderma croceum) were recombinantly expressed in E. coli and their products were analysed. Both phylogenetic analysis and EFI-EST analysis have very accurate prediction. The TPSs highlighted with a circle (“●”) were characterized in this study.

FIG. 25 shows the metal binding motif of the characterized TPSs in this study and in literature.

FIG. 26 shows crystal structures of homologue models for Agrped1_689675 and Agrped1_689675, where the substrate-binding pockets are highlighted. The model was generated using the Swiss Model homology-modeling server and alignment mode with 5nx6 and 5nx5 as templates. Protein models were visualized and aligned with their template structure using PyMol.

FIG. 27 shows the crystal structure of DXS (PDB ID: 2o1s), where the substrates and mutated amino acids are highlighted.

DETAILED DESCRIPTION OF THE PRESENT INVENTION

In a first aspect, the present invention refers to a bacterial strain comprising one or more vectors encoding a) one or more enzymes to produce one or more terpene precursors, and b) a fungal terpene synthase (FTPS).

It will be appreciated by a person skilled in the art that the one or more vectors comprise polynucleotide sequences that encode the one or more enzymes to produce one or more terpene precursors and FTPS.

The polynucleotides encoding the one or more enzymes to produce one or more terpene precursors and the FTPS may be located on separate vectors, on a single vector or combinations thereof. In one embodiment, the polynucleotides encoding the one or more enzymes to produce one or more terpene precursors are in a single vector and the polynucleotide encoding the FTPS is in a separate vector.

In one embodiment, the one or more vectors comprise one or more nucleotide sequences encoding the one or more enzymes and the FTPS, operably linked to a promoter.

In some embodiments, the promoter is a constitutive promoter or an inducible promoter. In a preferred embodiment, the promoter is an inducible promoter. Examples of inducible promoters include but are not limited to T7 RNA polymerase promoter, araBAD promoter, a lac promoter, a trp promoter and a Tac promoter (ptac) or the variants of these promoters.

In a preferred embodiment, the inducible promoter is T7 RNA polymerase promoter.

In one embodiment, the one or more enzymes to produce the one or more terpene precursors are part of the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway. It will be appreciated to a person of skill in the art that the DXP pathway is also referred to as the non-mevalonate pathway, the mevalonate-independent pathway or the 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (MEP/DOXP) pathway. The DXP pathway converts pyruvate and glyceraldehyde-3-phosphate to terpene precursors and the enzymes in this pathway include DOXP synthase (DXS), DXP reductoisomerase (DXR), 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD), 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF), HMB-PP synthase (ispG), HMB-PP reductase (IspH) and isopentenyl diphosphate isomerase (IDI).

In a preferred embodiment, the enzyme is 1-deoxyxylulose-5-phosphate synthase (DXS), isopentenyl diphosphate isomerase (IDI) or both.

In one embodiment, the DXS comprises the amino acid sequence set forth in SEQ ID NO: 6.

In some embodiments, the DXS may be genetically modified. The genetic modification may be a mutation at one or more amino acid positions of the amino acid sequence encoding the DXS. In some examples, the mutation is an amino acid substitution, insertion, deletion or combinations thereof.

In some embodiments, the genetically modified DXS has a higher solubility than an unmodified or wild-type DXS.

In some embodiments, the mutation is selected from the group consisting of H105T, E210D, Q459L, L415T and a combination thereof of SEQ ID NO: 6.

In a preferred embodiment, the mutation is H105T.

In another preferred embodiment, the mutation is E210D, Q459L and L415T.

In one embodiment, the genetically modified DXS comprises the amino acid sequence set forth in SEQ ID NO: 24 or 25.

In one embodiment, the DXS comprises an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to an amino acid sequence set forth in SEQ ID NO: 6, SEQ ID NO: 24 or 25.

In one embodiment, the one or more enzymes to produce the one or more terpene precursors is expressed at an elevated level compared to a wild type enzyme. The one or more enzymes may be genetically modified.

In some embodiments, the terpene precursors described herein is farnesyl pyrophosphate (FPP), geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP), or combinations thereof.

In a preferred embodiment, the terpene precursors are FPP and/or GPP.

The bacterial strain described herein comprises one more vectors encoding a fungal terpene synthase (FTPS). In a preferred embodiment, the FTPS is a monoterpene synthase or a sesquiterpene synthase. In a further preferred embodiment, the FTPS is a linalool synthase, a nerolidol synthase or a linalool and nerolidol synthase (LNS).

In some embodiments, the FTPS is isolated from Agrocybe aegerita, Agrocybe pediades, Galerina marginata, Hypholoma sublateritium, Dendrothele bispora, Moniliophthora roreri, Piloderma croceum, Sphaerobolus stellatus, Coprinopsis cinerea, Omphalotus olearius, Fomitopsis pinicola, Stereum hirsutum, Fusarium graminearum, Fusarium fujikuroi, Fusarium sporotrichioides, Aspergillus terreus, Penicillium roqueforti, Hypoxylon sp., Armillaria gallica, Botrytis cinerea, Daldinia eschscholzii or combinations thereof.

In one embodiment, the FTPS is isolated from Agrocybe aegerita, Agrocybe pediades, Galerina marginata, Hypholoma sublateritium, Hebeloma cylindrosporum or combinations thereof.

In a preferred embodiment, the FTPS is isolated from Agrocybe aegerita or Agrocybe pediades.

In some embodiments, the FTPS comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33 and SEQ ID NO: 34.

In some embodiments, the FTPS comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39.

In one example, the bacterial strain described herein contains an FTPS that is expressed at a higher level than a wild-type FTPS.

In some embodiments, the FTPS may be genetically modified. The genetic modification may be an amino acid substitution, insertion, deletion, C-terminal truncation, N-terminal truncation or combinations thereof. The mutation may be one or more mutations in the UP domain of the FTPS, one or more mutations in the DW domain of the FTPS, or both. The UP and DW domains would be understood by the skilled person to vary based on the fungal strain. In one example, the UP domain of the FTPS isolated from Agrped1_689675 (SEQ ID NO: 3) is characterized by amino acid positions 1-170. In another embodiment, the UP domain of the FTPS isolated from Agrped1_689671 (SEQ ID NO: 2) is characterized by amino acid positions 1-169. In yet another embodiment, the DW domain for the FTPS isolated from Agrped1_689675 (SEQ ID NO: 3) is characterized by amino acid positions 171-325. In yet another embodiment, the DW domain of the FTPS isolated from Agrped1_689671 (SEQ ID NO: 2) is characterized by amino acid positions 170-324.

In a preferred embodiment, the mutation is F204D, F204G, F204R, F204I, F204L, F204V or combinations thereof of SEQ ID NO: 3.

In some embodiments, the genetically modified FTPS comprises an amino acid sequence selected from the group consisting of SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16 SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22 and SEQ ID NO: 23.

In some embodiments, the FTPS comprises an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to amino acid sequences set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16, SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33 and SEQ ID NO: 34.

In some embodiments, the bacterial strain is modified or genetically modified.

In one embodiment, the bacterial strain described herein is Escherichia coli.

In one aspect, the present invention refers to a genetically modified 1-deoxyxylulose-5-phosphate synthase (DXS) enzyme, wherein the genetic modification is a mutation at one or more amino acid positions. In one embodiment, the mutation described herein is an amino acid substitution or insertion or deletion. In yet another embodiment, the mutation is selected from the group consisting of H105T, E210D, Q459L, L415T and a combination thereof of SEQ ID NO: 6.

In a preferred embodiment, the mutation is E210D, Q459L and L415T.

In another preferred embodiment, the mutation is H105T.

In another aspect, the present invention refers to a genetically modified DXS enzyme comprising an amino acid sequence as set forth in SEQ ID NO: 24 or SEQ ID NO: 25.

In yet another aspect, the present invention refers to a genetically modified DXS enzyme comprising an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to an amino acid sequence set forth in SEQ ID NO: 24 or SEQ ID NO: 25.

In one aspect, the present invention refers to a genetically modified fungal terpene synthase (FTPS), wherein the genetic modification is a mutation at one or more amino acid positions.

The genetically modified FTPS is modified relative to a wild type or unmodified FTPS. In one embodiment, the unmodified FTPS is isolated from Agrocybe aegerita, Agrocybe pediades, Galerina marginata, Hypholoma sublateritium, Hebeloma cylindrosporum or combinations thereof.

In a preferred embodiment, the unmodified FTPS is isolated from Agrocybe aegerita or Agrocybe pediades.

In some embodiments, the mutation described herein is an amino acid substitution, insertion, deletion, C-terminal truncation, N-terminal truncation or combinations thereof. The mutation may be one or more mutations in the UP domain of the FTPS, one or more mutations in the DW domain of the FTPS, or both. The UP and DW domains would be understood by the skilled person to vary based on the fungal strain. In one example, the UP domain of the FTPS isolated from Agrped1_689675 (SEQ ID NO: 3) is characterized by amino acid positions 1-170. In another embodiment, the UP domain of the FTPS isolated from Agrped1_689671 (SEQ ID NO: 2) is characterized by amino acid positions 1-169. In yet another embodiment, the DW domain for the FTPS isolated from Agrped1_689675 (SEQ ID NO: 3) is characterized by amino acid positions 171-325. In yet another embodiment, the DW domain of the FTPS isolated from Agrped1_689671 (SEQ ID NO: 2) is characterized by amino acid positions 170-324.

In a preferred embodiment, the mutation is selected from the group consisting of F204D, F204G, F204R, F2041, F204L and F204V of SEQ ID NO: 3.

In some embodiments, the genetically modified FTPS described herein is a linalool synthase, nerolidol synthase or both.

In one embodiment, the present invention refers to a genetically modified FTPS comprising an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to an amino acid sequence selected from the group consisting of: SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22 and SEQ ID NO:23.

In one aspect, the present invention refers to a method of producing a terpenoid comprising a) culturing the bacterial strain as described herein in an expression medium and b) isolating the terpenoid from said expression medium.

Culturing the bacterial strain in the expression medium will allow the expression of the one or more enzymes to produce one or more terpene precursors and expression of the FTPS.

In another aspect, the present invention refers to a method of producing a terpenoid comprising a) culturing a bacterial strain comprising a vector encoding the genetically modified FTPS as described herein in an expression medium and b) isolating the terpenoid from said expression medium.

The expression medium may be any culture medium that supports growth of the bacterial strain. The expression medium may comprise inducers capable of inducing the inducible promoter in the one or more vectors. The expression medium may also be an auto-inducing medium. In one example, the auto-inducing medium is ZYM5052. In other examples, the auto-inducing medium is lysogeny broth (LB), Terrific Broth (TB) or 2xPY.

The expression medium may be further supplemented with spherical C18 resin or Ni-nitrilotriacetic acid resin.

In one embodiment, the method described herein further comprises the step of isolating the FTPS from the bacterial cell and mixing the isolated FTPS with one or more terpene precursors to produce the terpenoid. The isolated FTPS may be mixed with the one or more terpene precursors in the same cell culture vessel or in a different vessel from the original culture. The FTPS may be isolated using a variety of methods. In some embodiment, the FTPS is isolated the bacterial cell by Ni-nitrilotriacetic acid resin, column based methods or both.

In another embodiment, the isolated FTPS described herein is further purified prior to mixing with one or more terpene precursors.

In yet another embodiment, the isolated FTPS is further mixed with one or more additional enzymes prior to mixing with one or more terpene precursors.

In one embodiment, the one or more additional enzymes described herein is Acetyl-CoA acetyltransferase, Hydroxymethylglutaryl-CoA synthase (HMGS), Hydroxymethylglutaryl-CoA synthase reductase (HMGR), IDI, melonate kinase (MK), Phosphomevalonate kinase (PMK) or mevalonate diphosphate decarboxylase (MVD1). In some embodiments, the Acetyl-CoA acetyltransferase is PhaA or atoB. [SF: any others?]

In one embodiment, terpenes or terpenoids may be produced using the FTPS of the present invention as follows: 1. Using crude cell lysate, the bacterial cells expressing only FTPS are harvested and lysed by freeze/thaw method and/or sonication method. The lysed cell supernatant containing soluble FTPS is mixed with substrates (GPP or FPP), 2.5 mM MgCl2 and 50 mM Tris/HCl buffer (pH 6.5-8.5) to produce terpenoids at 30-37° C. In another example, the FTPS will be purified from the bacterial cells by Ni-nitrilotriacetic acid resin and/or column-based method. The purified FTPS is mixed with substrates (GPP or FPP), 2.5 mM MgCl₂ and 50 mM Tris/HCl buffer (pH 6.5-8.5) to produce terpenoids at 30-37° C. In addition, the FTPS may be coupled into a multienzyme reaction, for example at pH 7.5 and at 30° C., by mixing the FTPS with other enzymes such as IDI, MK, PMK or mevalonate pyrophosphate decarboxylase (PMD) to convert mevalonate into terpenoids.

In one embodiment, the product of the method described herein is a monoterpenoid, sesquiterpenoid or a mixture of both. In some embodiments, the monoterpenoid is selected from the group consisting of β-myrcene, linalool, geranyl acetate and combinations thereof.

In some embodiments, the sesquiterpenoid is selected from the group consisting of Δ6-protoilludene, α-muurolene, γ-muurolene, β-cadinene, β-copaene, δ-cadinene, δ-cadinene, epizonarene, α-cubebene, cubebol, epicubenol, nerolidol, viridiflorol, viridiflorene, α-cadinol, α-epi-cadinol, β-selinene, α-selinene, T-muurolol, β-elemene, β-gurjunene, germacrene A, germacrene D and combinations thereof.

In a preferred embodiment, the product is Δ6-protoilludene, linalool, geranyl acetate or combinations thereof.

The present invention also discloses the use of the FTPS described herein to produce one or more terpenoids.

In some embodiments, the one or more terpenoids is selected from the group consisting of β-myrcene, linalool, geranyl acetate, Δ6-protoilludene, α-muurolene, γ-muurolene, β-cadinene, β-copaene, δ-cadinene, γ-cadinene, epizonarene, α-cubebene, cubebol, epicubenol, nerolidol, viridiflorol, viridiflorene, α-cadinol, α-epi-cadinol, β-selinene, α-selinene, T-muurolol, β-elemene, β-gurjunene, germacrene A, germacrene D, trans-β-ocimene, β-cubebene, α-isocomene, longifolene, cadina-3,5-diene, caryophyllene, α-humulene, cubenene, calamenene, cubenol, δ-cadinol, cadina-1(6), 4-diene and combinations thereof.

In another embodiment, the one or more terpenoids described herein is produced in vitro or in vivo. In some embodiments, the one or more terpenoids is produced in vivo in a bacterial cell, a yeast cell, a plant cell, an animal cell or a fungal cell. In one example, the bacterial cell is an E.coli cell. In another example, the yeast cell is a Saccharomyces cerevisiae or a Yarrowia lipolitica cell.

In another embodiment, the one or more terpenoids described herein is produced in vitro.

In some embodiments, the FTPS described herein is isolated from a bacterial cell, a yeast cell, a plant cell, an animal cell or a fungal cell, and mixed with one or more terpene precursors to produce the one or more terpenoids.

In another embodiment, the isolated FTPS is further mixed with one or more additional enzymes prior to mixing with one or more terpene precursors. In one example, the one or more additional enzymes is IDI, MK, PMK or PMD.

The present invention also discloses a vector comprising a polynucleotide sequence encoding a 1-deoxyxylulose-5-phosphate synthase (DXS) enzyme comprising an amino acid sequence set forth in SEQ ID NO: 6, or a genetically modified 1-deoxyxylulose-5-phosphate synthase (DXS) enzyme as described herein.

In another example, the present invention refers to a vector comprising a polynucleotide sequence encoding a fungal terpene synthase (FTPS) comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4 and SEQ ID NO:5, or a genetically modified fungal terpene synthase (FTPS) as described herein.

The polynucleotide sequences generated from amino acid sequences may be optimized for improved expression in a host cell or an expression vector. The DNA sequences may be generated from amino acid sequences to have optimised Codon Adaptation Index (>0.6) and GC percentage (40-60%). Codon usage frequency table may be based on a strain of bacterial cell, for example, on Escherichia coli K-12 MG1655 strain. In most cases, a guided random method based on a Monte Carlo algorithm may be used. However, manual adjustments may be introduced to remove certain regions with complex secondary structures or repeated sequences. It will generally be understood that various codon optimization methods may be employed to improve expression of a protein or polypeptide in a host cell or expression vector.

In one aspect, the present invention refers to an FTPS encoded by a polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39.

In another aspect, the present invention refers to an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO:39.

In some embodiments, the nucleic acid sequence has at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or, at least 99% or 100% identity to the nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39.

The bacterial strain as disclosed herein may be used to characterize a FTPS. In another embodiment, the FTPS may be characterized by a product produced by the FTPS, the activity of the FTPS, or both.

The invention illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Thus, for example, the terms “comprising”, “including”, “containing”, etc. shall be read expansively and without limitation. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.

Other embodiments are within the following claims and non-limiting examples. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

Experimental Section

Non-limiting examples of the invention and comparative examples will be further described in greater detail by reference to specific Examples, which should not be construed as in any way limiting the scope of the invention.

The fungal TPSs that have been cloned and functionally characterized are shown in Table 1.

TABLE 1 Published functionally characterized fungal terpene synthases. Accession or JGI Protein Abbre- ID viation Organisms Main product Minor products Reference  1 EAU89322 Cop1 Coprinopsis germacrene A (Agger et al., cinerea 2009)  2 EAU85264 Cop2 Coprinopsis germacrene A (Agger et al., cinerea 2009)  3 EAU88892 Cop3 Coprinopsis α-muurolene β-elemene, γ- (Agger et al., cinerea muurolene, 2009) germacrene D and δ-cadinene  4 EAU85540 Cop4 Coprinopsis δ-cadinene β-cubebene, (Agger et al., cinerea sativene, β- 2009) copaene, cubebol  5 EAU89298 Cop6 Coprinopsis α-cuprenene (Agger et al., cinerea 2009)  6 — Omp1 Omphalotus α-muurolene (Wawrzyn et olearius al., 2012)  7 — Omp3 Omphalotus α-muurolene β-elemene and (Wawrzyn et olearius selina-4,7-diene al., 2012)  8 — Omp4 Omphalotus δ-cadinene 16 different (Wawrzyn et olearius sesquiterpenes al., 2012)  9 — Omp5 Omphalotus γ-cadinene epi-zonarene (Wawrzyn et olearius al., 2012) 10 — Omp6 Omphalotus Δ6-protoilludene (Wawrzyn et olearius al., 2012) 11 — Omp7 Omphalotus Δ6-protoilludene (Wawrzyn et olearius al., 2012) 12 — Omp9 Omphalotus α-barbatene β-barbatene (Wawrzyn et olearius al., 2012) 13 — Omp10 Omphalotus trans-dauca- daucene (Wawrzyn et olearius 4(11),8-diene al., 2012) 14 — Fompil_84944 Fomitopsis α-cuprenene (Wawrzyn et pinicola al., 2012) 15 — Stehi_64702 Stereum Δ6-protoilludene (Quin et al., hirsutum 2013) 16 — Stehi_73029 Stereum Δ6-protoilludene (Quin et al., hirsutum 2013) 17 — Stehi_25180 Stereum Δ6-protoilludene (Quin et al., hirsutum 2013) 18 — Stehi_128 Stereum δ-cadinene β-copaene, (Quin et al., 017 hirsutum sativene, γ- 2013) muurolene, α- muurolene etc 19 — Stehi_159379 Stereum β-barbatene α-barbatene and (Quin et al., hirsutum β-barbatene 2013) 20 ACY69978 CLM1 Fusarium longiborneol (McCormick FgLS graminearum et al., 2010) 21 CCP20071.1 Ffsc6 Fusarium (−)-α-acorenol (Brock et al., fujikuroi 2013) 22 CCP20072.1 Ffsc4 Fusarium koraiol (Brock et al., fujikuroi 2013) 23 AAD13657 FsTDS Fusarium trichodiene (Rynkiewicz sporotrichioides et al., 2001) 24 AAF13264 AtARS Aspergillus aristolochene (Cane and terreus Kang, 2000) 25 AAA33694 PrARS Penicillium aristolochene (Hohn and roqueforti Plattner, 1989) 26 KJ433269 Hyp1 Hypoxylon sp. trans-nerolidol (Shaw et al., 2015) 27 KJ433270 Hyp2 Hypoxylon sp. δ-cadinene 21 other peaks (Shaw et al., 2015) 28 KJ433271 Hyp3 Hypoxylon sp. 1,8-cineole (C10) D-limonene (C10) (Shaw et al., 2015) 29 KJ433272 Hyp4 Hypoxylon sp. D-limonene (C10) 12 other peaks (Shaw et al., 2015) 30 KJ433273 Hyp5 Hypoxylon sp. β-ocimene (C10) sabinene (C10), (Shaw et al., α-bulnesene and 2015) unknown peaks 31 — Pro1 Armillaria Δ-protoilludene (Engels et al., gallica 2011) 32 CCT65043 STC3 Fusarium (+)-eremophilene (Burkhardt et fujikuroi al., 2016) 33 CCT75704 STC5 Fusarium (−)-guaia- (Burkhardt et fujikuroi 6,10(14)-diene al., 2016) 34 AAQ16575 BcBOT2 Botrytis cinerea presilphiperfolan- (Moraga et or 8β-ol al., 2016) BcPSPS 35 JGI ID: EC12- Daldinia Guaiene Pinene (C10) (Wu et al., 17536 PGS eschscholzii 2016) EC12 36 JGI ID: EC12-GS Daldinia Gurnunene (Wu et al., 315006 eschscholzii 2016) EC12 37 JGI ID: EC12-SS Daldinia Selinene (Wu et al., 24646 eschscholzii 2016) EC12 38 JGI ID: EC12-ILS Daldinia IsoLedene (Wu et al., 70183 eschscholzii 2016) EC12 39 JGI ID: CI4A-CS Hypoxylon sp. Caryophyllene (Wu et al., 6706 CI4A 2016) 40 JGI ID: CI4A-CPS Hypoxylon sp. Chamigrene Pinene (C10) (Wu et al., 322581 CI4A 2016) 41 JGI ID: CO27-CS Hypoxylon sp. Caryophyllene (Wu et al., 397991 CO27 2016) 42 JGI ID: CO27- Hypoxylon sp. Chamigrene Pinene (C10) (Wu et al., 392541 CPS CO27 2016) 43 JGI ID: EC38-CS Hypoxylon sp. Caryophyllene (Wu et al., 373976 EC38 2016) 44 JGI ID: EC38- Hypoxylon sp. Chamigrene Pinene (C10) (Wu et al., 328361 CPS EC38 2016)

Cultivation of Agrocybe aegerita and Analysis of its Fruiting Bodies

Agrocybe aegerita wildtype-strain AAE-3 was grown at 24° C. in the dark in modified crystallizing dishes (FIG. 1; lower dish: 70 mm in diameter, upper dish: 80 mm in diameter; glass pipe attached to the upper dish: outer diameter 16 mm, inner diameter 14 mm) with 16 mL 1.5% MEA (containing 15 g malt extract and 15 g agar per liter) and sealed with Parafilm. The ten days after the inoculation, the mycelium covered the complete agar surface. The Parafilm was removed and the samples were transferred to a climate chamber (24° C., 95% rH, 12/12 h day/night rhythm) and cultured on glass plates for further 16 days. Volatile organic compounds were collected by solid phase microextraction (SPME) using a divinylbenzene-carboxen-polydimethylsiloxane (50/30 μm DVB/CAR/PDMS) fiber. Beginning with day 10 after inoculation, volatiles were absorbed directly in the crystallizing dishes for 14 h (7/7 h day/night). This extraction was carried out every second day. For GC-MS analysis an Agilent Technologies 7890A gas chromatograph (Agilent Technologies, Waldbronn, Germany) equipped with a VF WAXms column (Agilent Technologies; 30 m×0.25 mm, 0.25 μm) and connected to an Agilent 5975C MSD Triple Axis mass spectrometer (MS) was used. Helium was used as gas carrier, with a flow rate of 1.2 ml×min⁻¹. Mass spectra were acquired in the mass range of 33 300 m/z. Ionisation was performed by electron impact at 70 eV with an ion source temperature set at 230° C. The SPME fiber was inserted into the injector of the gas chromatograph for thermal desorption in splitless mode for 1 min, with the injector temperature held at 250° C. The GC oven temperature was programmed to ramp from 40° C. (held for 3 min) to 240° C. (held for 7 min) at 5° C.×min⁻¹. Volatile compounds were identified by comparing mass spectra with data from the NIST14 database and matching determined retention indices with published ones. Furthermore, Cubeb oil and a humulene were used as standards.

Gas Chromatography-Mass Spectrometry Analysis of Terpenoids

Volatile compounds in the headspace were sampled at room temperature for 15 min by SPME with a DVB/CAR/PDMS (50/30 μm divinylbenzene/carboxen/polydimethylsiloxane) fiber (length 1 cm; Supelco, Steinheim, Germany). Compounds were desorbed in the split/splitless inlet (250° C. or 150° C.; SPME liner, 0.75 mm i.d.; Supelco) of an Agilent 7980B gas chromatography equipped with an Agilent 7200 accurate-mass quadrupole time-of-flight (GC/MS-TOF; Agilent Technologies, Singapore) for 1 min. In addition, for liquid culture analysis, dodecane (20% v/v) was used to extract the terpenoid produced in E. coli cultures. The obtained dodecane was diluted at 1:100 in hexane for GC-MS analysis. The GC/MS-TOF was equipped either with a VF-WAXms column (Agilent Technologies; 30 m×0.25 mm i.d., 0.25 μm film thickness) or a DB-5ms column (Agilent Technologies; 30 m×0.25 mm i.d., 0.25 μm film thickness), and the system was operated on the following conditions: (1) VF-WAXms, compounds were detected in split mode at split ratio of 10:1, the GC oven temperature was programmed to ramp from 80° C. (held for 2 min) to 240° C. (held for 5 min) at 10° C.×min⁻¹; (2) DB-5ms, compounds were detected in split mode at split ratio of 10:1, the GC oven temperature was programmed to ramp from 50° C. (held for 2 min) to 160° C. at 10° C.×min⁻¹, to 230° C. at 8° C.×min⁻¹ and finally to 320° C. (held for 3 min). Mass spectra were acquired in the mass range of 33 300 m/z at the acquisition rate of 2 spectra/s. Ionization was performed by electron impact at 70 eV with an ion source temperature set at 230° C.

Structural Identification of Terpenoids

Mass spectra obtained by electron ionization mode were used for initial compound identification by comparing them with the spectra of terpenoids in the National Institute of Standards and Technology (NIST) database and published terpene spectra. Furthermore, Kovats retention indices of compounds produced were identified by calibrating with GC-MS with a C8-C30 alkane mix and were compared to the published retention indices in literature or in the NIST database. Major terpene products were verified, whenever possible, by comparison of retention time and mass spectra with authentic standards or essential oils with known terpene compositions. Niaouli essential oil [viridiflorene 6 (10.1% w/w), viridiflorol 7 (18.1% w/w)], Cedrela woods oil [α-muurolene 5 (1% w/w), δ-cadinene 4 (11.7% w/w)], Cubeb oil [germacrene D (1% w/w), γ-muurolene 2 (4.2% w/w), β-cubebene (4.4% w/w), cubebol (15.2% w/w)], Amyris wood oil [β-elemene (germacrene A) (0.1% w/w), δ-cadinenol, 0.2%]. In addition, the structure of Δ6-protoilludene was further confirmed by nuclear magnetic resonance spectroscopy.

Functional Annotation for Terpene Synthases and its Gene Clusters in the Agrocybe aegerita Genome

All the predicted amino acid sequences of protein-coding genes present in the genome of the dikaryotic strain A. aegerita AAE-3 have been searched for homologues to already characterized sesquiterpene synthases of Coprinopsis cinerea, Omphalotus olearius and Stereum hirsutum by blastp using Geneious® (version 9.1.8, Biomatters Ltd., Auckland, New Zealand). The predicted TPSs genes were then manually annotated. In addition, antiSMASH analysis was performed using the BiosynML plugin for Geneious® to predict terpene gene clusters in the A. aegerita genome.

Cloning and Expression of Terpene Synthase Genes in E. coli

Candidate fungal TPS genes were synthesized by Integrated DNA technologies and codon-optimized for expression in E. coli. The genes were cloned into pET11a vector for expression under the control of the T7 promoter. The resulting plasmid was transformed into BL 21 strains carrying the plasmid p15A-cam-T7-dxs-idi which was redesigned from the plasmid pACM-T7-dxs-T7-idi-T7-ADS-ispA. Furthermore, the dxs in the plasmid was mutated to SL3 or SL5 (FIG. 2) to improve the solubility and activity. Single colony of the transformed E. coli cells was inoculated into 4 ml ZYM5052 auto-inducing medium (1% tryptone, 0.5% yeast extract, 25 mM Na2HPO4, 25 mM KH2PO4, 50 mM NH4Cl, 5 mM Na2SO4, 2 mM MgSO4, 0.5% glycerol, 0.05% glucose, 0.2% α-lactose) (Studier, 2005) with ampicillin (100 mg/L) and chloramphenicol (33 mg/L). After 14 h of cultivation at 28° C. and 250 rpm on a shaking incubator, the culture fluid was transferred into a 20 mL headspace screw top vials (Merck) and the headspace was sampled at 50° C. for 15 min by SPME.

Homology Searches and Phylogenetic Tree Construction

The 11 A. aegerita TPSs were used to search other fungal TPSs in Basidiomycota and Ascomycota genomes sequenced and published by the Joint Genome Institute under the Fungal Genomics Program (http://genome.jgi-psf.org/programs/fungi/index.jsf) and in the UniProt database by Basic Local Alignment Search Tool program (http://www.uniprot.org/blast/). In addition, the previously published 392 basidiomycota TPSs were incorporated. The combined TPS candidates were manually inspected for duplicate sequences, erroneous protein predictions, such as incomplete sequences that deviated from the expected protein length (200-800 aa, except for two putative TPSs, Disac1_349444 and EXIGL_831178) or lacking the conserved metal-binding DxxxD and NSE/DTE triad, or with predicted additional domains (such as geranylgeranyl pyrophosphate synthase functions). Upon identification of putative TPS amino acid sequences, their alignments were performed using Clustal Omega and phylogenetic analyses were conducted with the Neighbor-Joining method using Clustal Omega or MEGA version 7.0.26.

Analysis of TPS Homologues by Sequence Similarity Networks

The curated fungal TPSs were analyzed by Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) web tool (http://efi.igb.illinois.edu/efi-est/) to generate sequence similarity networks (SSNs). The resulting SSNs were visualized using the open source software Cytoscape (http://www.cytoscape.org/). Inspection of the resulting SSNs is essential to obtain isofunctional clusters. Based on the SSNs generated by EFI-EST and sequentially varying a series of database-independent alignment score, a group of putative isofunctional groups (PIGs) were obtained. The data of PIGs and traditional phylogenetic trees were compared to select the putative isofunctional TPSs. Here, the three novel TPSs (viridiflorol synthase AAE3_13291, viridiflorene synthase AAE3_12839, and linalool/nerolidol synthase AAE3_9435) were chosen to probe other putative isofunctional TPSs which were further validated by experiments.

Δ6-Protoilludene Extraction and NMR Validation of its Structure

The AAE3_10454 recombinant E. coli strain was cultured in 200 mL of ZYM5052 auto-inducing medium, supplemented with 100 mg of the spherical C18 resin (VersaFlash spherical C18 bonded flash silica 45-75 um, Sigma-Aldrich). After 24 h of cultivation at 28° C. and 150 rpm, the cell culture was manually filtered by a C18 cartridge and was subsequently washed twice by deionized water. After filtration, the cells and liquid media were removed from the C18 cartridge. The terpene compound bound to the C18 resin was eluted by 10 mL of hexane. The eluted terpene solution was evaporated at 4° C. and subsequently analyzed on a Bruker DRX-400 NMR spectrometer with Cryoprobe, using 5-mm BBI (1H, G-COSY, multiplicity-edited G-HSQC, and G-HMBC spectra) or BBO (13C spectra) probe heads equipped with z-gradients. Spectra were calibrated to residual protonated solvent signals CHCl3 δH 7.24 and CDCl3 δC 77.23). The terpene compound was verified as Δ6-protoilludene by comparing the NMR spectral data with those reported in the literature.

EXAMPLE 1

Engineering an E. coli Strain for TPS Characterization.

The wild-type E. coli BL21 produces little amount of terpene precursors (GPP and FPP), therefore, it is not suitable as a TPS characterization platform. To improve the detection sensitivity and accuracy, DXS and IDI were overexpressed to improve the intracellular precursors (FIG. 3). Distinct from existing methods, two DXS mutants (SL3 and SL5) were identified based on random mutagenesis and screening. As shown in FIG. 2, SL3 and SL5 had higher solubility over wild-type DXS, and therefore a higher activity than wild-type DXS. More importantly, SL5 has higher specific activity than wild-type DXS (FIG. 2B). As a result, the lycopene yield in the strain overexpressing SL3 or SL5 was higher than that of wild-type DXS. Here, lycopene was used as an indicator to prove that GPP and FPP in the strains (SL3 and SL5) are higher. With the DXS mutants, the detection sensitivity of the cell platform is further improved. Hence, the E. coli strain (SL3 or SL5) was used as the platform for characterization of TPSs. FIG. 27 shows a crystal structure of DXS where beneficial mutations have been highlighted. The mutants are related to the improved solubility of DXS by enzyme engineering approach. The ligand pyrophosphate was shown in salmon color and magnesium was in firebrick color.

EXAMPLE 2

Analysis of Terpenes Produced in A. aegerita

To obtain an estimate of terpenes produced in A. aegerita, volatile compounds produced by its liquid cultures were analyzed. The illudin precursor, Δ(6)-protoilludene 1, was a dominant metabolite produced by A. aegerita (FIG. 1). In addition, small amount of α-ioscomene^(#), α-, β-cubebene, β-copaene, γ-muurolene 2, δ-cadinene 4, β-selinene^(#) 9, cubenene, epicubenol 10 and cubenol (FIGS. 4 and 5 for chemical structure and mass spectra of all the terpene identified in the study, respectively) were observed after 26 days of culture. The results proved that the mushroom, A. aegerita produces structurally diverse terpenes.

EXAMPLE 3

The Sesquiterpenome of A. aegerita

During fructification of A. aegerita 20 putative terpenoids were detected by means of GC/MS analysis, of which the tentatively identified Δ6-protoilludene^(#) was the most prominent compound (FIG. 1). Other major compounds were α-cubebene, α-isocomene, β-cubebene and δ-cadinene (Compound structures in FIG. 4, the mass spectra in FIG. 5). The blastp search for putative STSs present in the genome of A. aegerita revealed 11 genes (Table 2 and FIG. 6). Seven of the TPSs cluster with already known basidiomycete TPSs into at least three different groups. Four putative TPSs (AAE3_09008, AAE3_06743, AAE3_04444 and AAE3_05024) compile to an own cluster (FIG. 6). Four of the STS genes (AAE3_10454, AAE3_12839, AAE3_04120 and AAE3_13291) are part of clusters consists amongst other of two to five P450 monooxygenases.

TABLE 2 Details on Agrocybe aegerita STSs genes. gene number protein Protein ID scaffold gene start gene stop length of introns length 04120 2 9,526 11,372 1,847 6 659 04120 short 2 10,043 11,372 1,330 5 346 04444 2 1,033,830 1,035,120 1,291 4 353 09164 4 405,253 406,500 1,248 4 342 13190 8 106,456 107,896 1,441 6 358 13291 8 437,487 439,057 1,571 5 430 05024 21 111,488 112,812 1,325 4 355 06595 28 328,403 329,611 1,209 3 346 06743 29 231,813 233,188 1,376 4 372 09008 39 347,841 349,082 1,242 6 308 10454 49 17,315 18,741 1,427 5 387 12839 70 55,035 56,437 1,403 4 389

EXAMPLE 4

Characterization of 11 Predicted Sesquiterpene Synthases

All 11 predicted STSs were codon optimized and cloned into the pET vector, which was transformed into an engineered E.coli BL21 strain overproducing farnesyl pyrophosphate (FPP), the sesquiterpene precursor. Compounds tentatively identified on basis of their retention index (RI) and mass spectra in comparison to those in the literature and databases as described in the methods are marked with a hashmark (#).

All STSs (TPSs) except AAE3_09008 and AAE3_05024 gave rise to one or more sesquiterpenes in liquid cultures of the corresponding E. coli clone (FIG. 7 (DB-5ms column), FIG. 8 (VFWAXms column) and Table 3). AAE3_04120 and AAE3_10454 produced the same sesquiterpene as the only product. NIST database search and a comparison with mass spectra of fungal sesquiterpenes from previous reports (FIG. 5 and Table 3) revealed this compound could be Δ6-protoilludene 1. And its structure was further validated by the NMR analysis which had the identical spectrum with previous report (FIG. 9). Δ6-protoilludene is the precursor for illudins that have shown anti-tumor and antimicrobial effects. Till now, six Δ6-protoilludene synthases from three fungal species have been reported, Omp6 and Omp7 from Omphalotus olearius, Pro1 from Armillaria gallica and Stehi1_25180, Stehi1_64702 and Stehi1_73029 from Stereum hirsutum. Interestingly, AAE3_04120 and AAE3_10454 form a closely related subgroup with the six reported synthases in the phylogenetic clustering (FIG. 1), indicating that the 6-protoilludene synthases are highly related among different fungal species.

TABLE 3 Terpene products of the TPSs in this study. SPME DB5 (Non-polar) VFWAXms (Polar) data Area Area Gene Products % RI Literature RI % RI Literature RI AAE3_04120 Δ6-protoilludene 100% 1391 1393 100% 1513 — AAE3_04444 β-elemene  8% 1400 1391 ± 2 (521) — — 1591 ± 9 (259) γ-muurolene  33% 1487 1477 ± 3 (392)  30% 1706 1692 ± 12 (165) β-selinene  18% 1509 1486 ± 3 (349) — — 1717 ± 13 (167) α-selinene  14% 1515 1517 — — 1656 ± 0 (2) β-cadinene  21% 1518 1518 ± 10 (30)  22% 1733 1720 ± N/A (1) δ-cadinene  6% 1529 1524 ± 2 (751)  4% 1772 1758 ± 13 (374) α-epi-Cadinol — — —  9% 2213 2169 ± 16 (145) AAE3_06595 γ-muurolene  5% 1489 1477 ± 3 (392) — — 1692 ± 12 (165) β-selinene  5% 1508 1486 ± 3 (349) — — 1717 ± 13 (167) α-muurolene  7% 1511 1499 ± 3 (427)  8% 1739 1726 ± 13 (198) α-Selinene  5% 1514 1517 — — 1656 ± 0 (2) δ-cadinene  60% 1529 1524 ± 2 (751)  57% 1772 1758 ± 13 (374) T-muuroloI  8% 1659 —  13% 2198 2186 ± 16 (140) α-cadinol  10% 1671 —  18% 2243 2226 ± 9 (182) AAE3_6743 γ-muurolene  27% 1488 1477 ± 3 (392)  14% 1706 1692 ± 12 (165) β-cadinene  13% 1516 1518 ± 10 (30)  13% 1733 1720 ± N/A (1) δ-cadinene  13% 1527 1524 ± 2 (751)   6% 1772 1758 ± 13 (374) Unknown  44% 1650 —  52% 2176 sesquiterpene alcohol AAE3_9164 β-myrcene*  10%  989 991 ± 2 (841)  7% 1172 1161 ± 7 (569) β-copaene — — —  2% 1610 1586 ± 12 (15) α-cubebene  8% 1358 1351 ± 2 (338)  1% 1469 1463 ± 6 (186) γ-muurolene  15% 1487 1477 ± 3 (392)  8% 1677 1692 ± 12 (165) δ-cadinene  37% 1531 1524 ± 2 (751)  59% 1772 1758 ± 13 (374) epizonarene  13% 1538 1501 ± 4 (28)  8% 1677 1677 ± 1 (15) Unknown  9% 1548 —  4% 1736 1786 ± 13 (65) sesquiterpene epicubenol  8% 1660 1627 ± 2 (144)  7% 2076 2067 ± 21 (67) cubebol — — —  7% 1951 1957 AAE3_10454 Δ6-protoilludene 100% 1392 0 100% 1513 — AAE3_12839 δ-eIemene  2% 1345 1338 ± 2 (221) — — 1470 ± 9 (86) (+)-aromadendrene  7% 1457 1440 ± 1 (5) — — 1635 ± 2 (3) viridiflorene  82% 1508 1493 ± 4 (114)  81% 1712 1697 ± 7 (76) Unknown  9% 1514 — — — — sesquiterpene AAE3_13190 γ-muurolene  22% 1489 1477 ± 3 (392)  9% 1706 1692 ± 12 (165) (−)-germacrene D — — —  4% 1730 1710 ± 14 (325) a-muurolene  32% 1512 1499 ± 3 (427)  20% 1740 1726 ± 13 (198) δ-cadinene  24% 1529 1524 ± 2 (751)  24% 1772 1758 ± 13 (374) Cubenol — — —  4% 2076 2080 ± 4 (65) δ-cadinol/δ-cedrol  21% 1662 1645  24% 2209 2187 ± 10 AAE3_13291 viridiflorene  42% 1509 1493 ± 4 (114)  9% 1714 1697 ± 7 (76) viridiflorol*  58% 1617 1591 ± 2 (198)  91% 2099 2095 ± 10 (108) Denbil_816208 vindiflorene  31% 1509 1493 ± 4 (114)  8% 1714 1697 ± 7 (76) viridiflorol*  57% 1617 1591 ± 2 (198)  92% 2099 2095 ± 10 (108) Sphst_47084 viridiflorene  32% 1509 1493 ± 4 (114)  8% 1714 1697 ± 7 (76) viridiflorol*  58% 1617 1591 ± 2 (198)  92% 2099 2095 ± 10 (108) Pilcr_825684 β-elemene  7% 1401 1391 ± 2 (521) — — 1591 ± 9 (259) Unknown  12% 1490 — — — — sesquiterpene Viridiflorene  6% 1509 1493 ± 4 (114)  8% 1714 1697 ± 7 (76) epi-α-Selinene  8% 1514 1485 ± N/A (1)  12% 1726 1725 γ-cadinene  45% 1529 151 ± 2 (485)  30% 1774 1765± 11 (199) Unknown  15% 1538 — — — — sesquiterpene Galma_104215 β-gurjunene  83% 1441 1432 ± 3 (234)  81% 1673 1669 ± 17 (14) Unknown  10% 1439 —  12% 1634 — sesquiterpene

The E. coli strains expressing AAE3_0444 (SEQ ID NO: 27) and AAE3_6743 (SEQ ID NO: 29) produced several sesquiterpene compounds (FIG. 7, FIG. 8 and Table 3). γ-Muurolene 2 and β-cadinene^(#) 3 are the main products of AAE3_0444, together accounting for >50% of the total sesquiterpenes detected. In addition, small amounts of β-selinene^(#) 9, α-selinene^(#) 13, β-elemene (germacrene A) 11 and δ-cadinene 4 (verified by Cubeb essential oil, FIGS. 10 and S7) were detected in the headspace of AAE3_0444 culture. AAE3_6743 produced an unknown sesquiterpenol as the main product, together with small amounts of γ-muurolene 2 (27%), β-cadinene^(#) 3 (13%) and δ-cadinene 4 (13%).

A wide variety of sesquiterpenes were detected for the E. coli culture expressing AAE3_09164 (SEQ ID NO: 30) (FIG. 7, FIG. 8 and Table 3). Among them, δ-cadinene 4 (37%) was main product, together with γ-muurolene 2 (15%), epizonarene^(#) (13%), epicubenol^(#) 10 (8%), α-cubebene^(#) (8%) and many uncharacterized minor products. In addition, cubebol (6.7%, Table 3) was detected by VFWAXms (but not by DB5 column) and verified by Cubeb essential oil (FIG. 10). Interesting, a noticeable amount of the monoterpene β-myrcene (10%, verified by authentic standard, FIG. 12) was detected in the headspace of AAE3_09164 culture, despite that the E. coli strain produced only little amount of the monoterpene precursor geranyl pyrophosphate (GPP). The results suggested AAE3_09164 could be a bi-functional enzyme that is able to use both FPP and GPP as substrates to synthesize sesquiterpenes and monoterpenes, respectively. Similar bi-functional TPSs were reported previously in the ascomycete family Hypoxylaceae, such as Hyp4, Hyp5 from Hypoxylon sp. and EC12-PGS from Daldinia eschscholzii. In the phylogenetic analysis of the deduced AAE3_09164 amino acid sequence clustered together with Cop4, Omp4 and Stehi1_128017 enzymes (FIG. 13). Indeed, all of these enzymes including AAE3_09164 are highly promiscuous enzymes with δ-cadinene 4 as a common major product.

The E. coli strain expressing AAE3_13190 (SEQ ID NO: 33) produced four major products, α-muurolene 5 (32%) and γ-muurolene 2 (22%), δ-cadinene 4 (24%) and δ-cadinol^(#) 8 (21%) (FIGS. 7, 8, 10 and 11 and Table 3). In addition, there were at least six other minor sesquiterpene products, including (−)-germacrene D (Table 3) and verified by verified by Cubeb essential oil (FIG. 10). According to phylogenetic clustering in FIG. 13, AAE3_13190 is closely related to Cop3 from Coprinopsis cinerea and Omp3 from Omphalotus olearius. Consistently, all of them produced α-muurolene 5 as the major product. The major product for the E. coli culture expressing AAE3_06595 (SEQ ID NO: 28) was δ-cadinene 4 (60% of total terpenes). In addition, a few minor sesquiterpene compounds were also detected for AAE3_06595 culture including γ-muurolene 2, β-selinene^(#) and T-muurolor. The enzymes Cop1 and Omp2 are closely related to AAE3_06595. However, Omp2 was not functional in E. coli, and δ-cadinene 4 was only one minor product of Cop1 whose main product was β-elemene.

The major product of AAE3_12839 (SEQ ID NO: 34) was viridiflorene 6. In contrast, the E. coli strain expressing AAE3_13291 (SEQ ID NO: 32) produced viridiflorol 7 as the major product (viridiflorol 7 and viridiflorene 6 were confirmed by Niaouli essential oil, FIG. 14), with small amount of viridiflorene 6 (8.6% with VFWAXms in Table 3 and FIG. 8). Here, the data of VFWAXms column instead of DB5 column was used to quantify viridiflorol 7, as the quantification of viridiflorol 7 in DB5 was inaccurate with a significantly lower signal than viridiflorene 6 (FIG. 7 and Table 3). To our knowledge, no viridiflorene synthase or viridiflorol synthase has been reported in fungi. Even in plants, only six viridiflorene synthases were identified from Solanum lycopersicum and Nicotiana tabacum (Common tobacco). The alignment of AAE3_12839 and the tomato viridiflorene synthase indicated that there was limited sequence similarity (FIG. 15). Similarly, AAE3_13291 shares only 11% identity and less than 30% similarity with the viridiflorol synthase from Melaleuca quinquenervia, which is the only viridiflorol synthase reported so far (FIG. 16).

Furthermore, the identified TPSs in A. aegerita shared the same first cyclization step with TPSs in C. cinerea and O. olearius. For Δ-6-protoilludene synthase (AAE3_4120 (SEQ ID NO: 26) and AAE3_10454 (SEQ ID NO: 31)), viridiflorene synthase (AAE3_12839 (SEQ ID NO: 34)) and viridiflorol synthase (AAE3_13291 (SEQ ID NO: 32)), they all proceed through 1,11 cyclization of FPP to form tricyclic sesquiterpenes (FIG. 17). In contrast, other TPSs (AAE3_04444 (SEQ ID NO: 27), AAE3_6595 (SEQ ID NO: 28), AAE3_9164 (SEQ ID NO: 30), AAE3_13190 (SEQ ID NO: 33) and AAE3_6743 (SEQ ID NO: 29)) preferentially catalyze a 1,10 cyclization of FPP to form bicyclic sesquiterpenes.

EXAMPLE 5

Analysis of Fungal Genome for TPS Functional Study

The results in FIGS. 7 and 13 reinforced that certain types of fungal TPSs have highly conserved sequences fortified by identical products, such as eight characterized Δ6-protoilludene synthases and four characterized δ-cadinene synthases. Thus, phylogenetic analysis provides a predictive framework to identify novel terpene synthases with novel or similar functions. The predictive accuracy of the model increases as the number of experimentally characterized TPSs accumulates. Previously, three of the Δ6-protoilludene synthases (Stehi1_25180, Stehi1_64702 and Stehi1_73029 from S. hirsutum) were correctly predicted and validated through bioinformatic analysis. Since then, the genomes of many new fungal species have been sequenced but their TPS genes have not been studied. Here, the aim was to establish a new predictive framework for the functional study of uncharacterized fungal TPSs with the new characterized A. aegerita TPSs and previously studied fungal TPSs. Through BLAST search in fungal genome database at the Joint Genome Institute (JGI, http://genome.jgi-psf.org/programs/fungi/index.jsf) and in The Universal Protein Resource (UniProt, http://www.uniprot.org/), about 2,000 putative TPS genes was uncovered. After a series of curation (as described in methods), a total of 1,408 putative TPSs from 85 Basidiomycota and 239 Ascomycota genomes were obtained (Table 4). On average, Basidiomycota have an average of 10-15 TPSs per genome (800 TPSs from 84 Basidiomycota) but about 80% Ascomycota have only 1-3 TPSs per genome (594 TPSs from 236 Ascomycota).

TABLE 4 The information about 1408 putative fungal TPSs in this study. Ascomycota Basidiomycota Aaosphaeria arxii Agaricus bisporus Aaoar1_459904 Agabi_varbisH97_2_119105 Acephala macrosclerotiorum Agabi_varbisH97_2_144791 Aciaci1_473652 Agabi_varbisH97_2_149463 Acremonium strictum Agabi_varbisH97_2_195544 Alternaria alternata Agabi_varbisH97_2_73543 Altal1_1080498 Agabi_varbur_1_109605 Alternaria brassicicola Agabi_varbur_1_126555 Altbr1_7288 Agabi_varbur_1_130532 Amniculicola lignicola Agabi_varbur_1_46681 Amnli1_450732 Agabi_varbur_1_61902 Amore1_23054 Agabi_varbur_1_76352 Ampelomyces quisqualis Agabi_varbur_1_79290 Ampqui1_550807 Agrocybe aegerita Anthostoma avocetta AAE3_04120 Antav1_377590 AAE3_04444 Antav1_383196 AAE3_05024 Antav1_400494 AAE3_06595 Antav1_445568 AAE3_06743 Antav1_446501 AAE3_09008 Antav1_453578 AAE3_09164 Antav1_468055 AAE3_10454 Antav1_472246 AAE3_109435 Antav1_476690 AAE3_12839 Antav1_484797 AAE3_13190 Antav1_504933 AAE3_13291 Apiospora montagnei Agrocybe pediades Apimo1_107765 Agrped1_109003 Apimo1_109481 Agrped1_640059 Aplosporella prunicola Agrped1_665597 Aplpr1_315168 Agrped1_689671 Arthrobotrys oligospora Agrped1_689675 Artol1_6616 Agrped1_693394 Arthroderma benhamiae Agrped1_705454 Artbe1_2427 Agrped1_749682 Ascocoryne sarcoides Agrped1_804989 Ascsa1_1273 Agrped1_804996 Ascsa1_6084 Agrped1_820868 Aspergillus aculeatinus Amanita muscaria Aspacu1_414218 M378_161967 Aspacu1_433825 M378_167361 Aspergillus brasiliensis M378_181109 Aspbr1_199648 M378_186936 Aspergillus brunneoviolaceus M378_457656 Aspbru1_469179 M378_74452 Aspergillus calidoustus M378_78547 Aspcal1_764165 M378_9904 Aspcal1_767797 Armillaria gallica Aspcal1_768162 Pro1 Aspcam1_281412 Auricularia delicata Aspcam1_337372 Aurde1_106904 Aspergillus carbonarius Aurde1_129583 Aspca3_517619 Aurde1_138561 Aspc11_4114 Aurde1_166047 Aspergillus costaricaensis Aurde1_173663 Aspcos1_212514 Aurde1_56959 Aspcos1_272862 Aurde1_61813 Aspergillus fijiensis Aurde1_62781 Aspfij1_393093 Aurde1_73423 Aspergillus flavus Aurde1_73447 Aspfl1_36410 Aurde1_73578 Aspergillus heteromorphus Aurde1_75612 Asphet1_431105 Aurde1_81767 Aspergillus homomorphus Aurde1_90621 Asphom1_411924 Aurde1_97553 Aspergillus ibericus Auricularia subglabra Aspibe1_454210 AURDE_130623 Aspergillus indologenus Bjerkandera adusta Aspind1_388535 Bjead1_1_105488 Aspergillus kawachii Bjead1_1_117829 Aspka1_1_17804 Bjead1_1_156307 Aspka1_1_20838 Bjead1_1_158616 Aspergillus lacticoffeatus Bjead1_1_166045 Asplac1_345547 Bjead1_1_172777 Asplac1_444313 Bjead1_1_337295 Aspergillus luchuensis Bjead1_1_53082 Aspfo1_40412 Bjead1_1_54261 Aspfo1_48364 Bjead1_1_54262 Aspfo1_701161 Bjead1_1_64972 Aspergillus neoniger Botryobasidium botryosum Aspneo1_451579 Botbo1_115253 Aspergillus niger Botbo1_147563 Aspni_bvT_1_291648 Botbo1_150401 Aspni_bvT_1_339193 Botbo1_177898 Aspni_DSM_1_158481 Botbo1_189629 Aspni_DSM_1_165991 Botbo1_35044 Aspni_NRRL3_1_492 Calocera cornea Aspni_NRRL3_1_8436 CALC0_485200 Aspni_NRRL3_1_8732 Calocera viscosa Aspni7_1085752 CALVI_546272 Aspni7_1155978 CALVI_549316 Aspergillus nomius CALVI_565570 Aspnom13137_1_4577 Ceriporiopsis subvermispora Aspnom13137_1_5237 Cersu1_100300 Aspnom13137_1_5921 Cersu1_107906 Aspergillus novofumigatus Cersu1_108146 Aspoch1432_1_2847 Cersu1_113927 Aspergillus oryzae Cersu1_114263 Aspor1_10090 Cersu1_116249 Aspergillus phoenicis Cersu1_126560 Aspph1_338445 Cersu1_161387 Aspergillus piperis Cersu1_162846 Asppip1_454731 Cersu1_162851 Aspergillus sclerotiicarbonarius Cersu1_52233 Aspscle1_371398 Cersu1_71514 Aspergillus steynii Cersu1_78286 Aspste1_453294 Cersu1_83362 Aspergillus terreus Cersu1_85360 Aspte1_5331 Cersu1_95867 Aspergillus udagawae Cersu1_96486 Aspuda1_1612 Cersu1_98094 Aspuda1_4266 ter14 Aspergillus vadensis Coniophora puteana Aspvad1_340387 Conpu1_102165 Aspvad1_341847 Conpu1_102220 Aspwe1_186729 Conpu1_118913 Aspwe1_691717 Conpu1_137465 Aureobasidium pullulans Conpu1_152083 Aurpu_var_mel1_89219 Conpu1_155138 Baudoinia compniacensis Conpu1_156845 Bauco1_152112 Conpu1_15871 Bimuria novae-zelandiae Conpu1_168606 Biscogniauxia nummularia Conpu1_170276 Bisnum1_472611 Conpu1_47697 Bisnum1_480590 Conpu1_50941 Bisnum1_560481 Conpu1_58009 Bisnum1_595288 Conpu1_58901 Bisnum1_611126 Conpu1_58994 Bisporella sp. Conpu1_60451 Bissp1_639301 Conpu1_62719 Bissp1_741721 Conpu1_62911 BcBOT2 Conpu1_63003 Bysci1_371003 Conpu1_75631 Cadophora sp. Conpu1_88505 Cadsp1_422591 Conpu1_92191 Caloscypha fulgens Coprinopsis cinerea Calful1_769187 CC1G_03587 Capronia epimyces Cop1 Capep1_3727 Cop2 Chaetomium globosum Cop3 CHGG_03509 Cop4 Chalara longipes Cop5 Chalo1_381634 Cop6 Chalo1_464358 Cylindrobasidium torrendii Cladophialophora bantiana CYLTO_347245 Claba1_132379 CYLTO_369585 Cladophialophora psammophila CYLTO_380537 Claps1_13034 CYLTO_384541 Cladorrhinum bulbillosum CYLTO_400743 Clabul1_1016528 CYLTO_405471 Clabul1_76434 CYLTO_436484 Clabul1_847239 CYLTO_442632 Clathrospora elynae CYLTO_452977 Clael1_510577 CYLTO_453006 Coccomyces strobi Dacryopinax primogenitus Cocst1_631366 DACRY_34691 CocheC4_1_36610 Dacryopinax sp. CocheC5_3_10970 Dacsp1_109687 Cochliobolus miyabeanus Dacsp1_81212 Cocmi1_93348 Dacsp1_96371 Cochliobolus sativus Daedalea quercina Cocsa1_348577 DAEQU_261749 Colac2_589620 DAEQU_662879 Co1ac2_693029 DAEQU_663038 Co1ac2_720284 DAEQU_677968 Co1ac2_722687 DAEQU_696090 Co1ac2_756572 DAEQU_737681 Colletotrichum caudatum DAEQU_745062 Colca1_582509 DAEQU_769721 Colca1_613400 DAEQU_811112 Colletotrichum cereale Dendrothele bispora Colce1_637756 Denbi1_650172 Colce1_710743 Denbi1_654460 Colce1_751683 Denbi1_659367 Colce1_753190 Denbi1_667929 Colletotrichum eremochloae Denbi1_678334 Coler1_553160 Denbi1_689487 Coler1_633162 Denbi1_690253 Coler1_645427 Denbi1_692356 Colletotrichum fioriniae Denbi1_693874 Colfi1_276541 Denbi1_750040 Colfi1_276864 Denbi1_792287 Colfi1_283382 Denbi1_816208 Colfi1_285486 Denbi1_818935 Colfi1_288712 Denbi1_824130 Colletotrichum godetiae Denbi1_855029 Colgo1_546119 Denbi1_866377 Colgo1_562331 Denbi1_873510 Colgo1_645279 Denbi1_896419 Colgo1_696718 Diaporthe helianthi Colgo1_730749 DHEL01_07884 Colletotrichum higginsianum Dichomitus squalens Colhig2_12235 Dicsq1_104353 Colhig2_13496 Dicsq1_138476 Colhig2_6613 Dicsq1_144469 Colhig2_7207 Dicsq1_146430 Colhig2_9460 Dicsq1_147637 Collu1_212508 Dicsq1_159719 Collu1_590124 Dicsq1_170641 Collu1_79349 Dicsq1_181048 Colletotrichum navitas Dicsq1_57723 Colna1_600097 Dicsq1_58025 Colna1_637650 Dicsq1_63165 Colny1_1016018 Dicsq1_80177 Colny1_1018170 Dicsq1_80370 Colny1_1022050 Dicsq1_86568 Colny1_1022440 Exidia glandulosa Colletotrichum orchidophilum EXIGL_605329 Color1_5151 EXIGL_611671 Color1_6973 EXIGL_620059 Color1_848 EXIGL_664938 Colletotrichum phormii EXIGL_673075 Colph1_306140 EXIGL_673208 Colph1_417792 EXIGL_677911 Colph1_464784 EXIGL_677941 Colph1_466218 EXIGL_680198 Colph1_479875 EXIGL_681577 Colph1_516153 EXIGL_688085 Colsa 1_939591 EXIGL_713320 Colsa 1_940033 EXIGL_743228 Colsa1_941201 EXIGL_750528 Colsa 1_942596 EXIGL_767126 Colsa 1_948955 EXIGL_769607 Colsa 1_950600 EXIGL_769609 Colletotrichum simmondsii EXIGL_770624 Colsi1_971930 EXIGL_773846 Colsi1_972523 EXIGL_831178 Colsi1_972624 Fibroporia radiculosa Colsi1_976172 FIBRA_00633 Colsi1_976953 FIBRA_00800 Colsi1_979039 FIBRA_05385 Colsi1_981054 FIBRA_05798 Colsi1_981282 FIBRA_06228 Colsi1_983009 FIBRA_06230 Colso1_559351 FIBRA_06895 Colletotrichum sublineola FIBRA_07171 Colsu1_648985 FIBRA_07173 Colsu1_724576 Fibulorhizoctonia sp. Colzo1_706815 FIBSP_768030 Coniella sp FIBSP_820394 Pilidi1_186199 FIBSP_832548 Coniochaeta ligniaria FIBSP_943511 Conli1_10674 Fistulina hepatica Conli1_1914 FISHE_34696 Conlig1_583628 FISHE_45426 Conlig1_658201 FISHE_46267 Coniochaeta sp. FISHE_66255 ConPMI546_932510 Fomitiporia mediterranea ConPMI546_934988 Fomme1_105378 Coniosporium apollinis Fomme1_109318 Conap1_98915 Fomme1_112446 Corollospora maritima Fomme1_170128 Corma2_707499 Fomme1_17224 Cryphonectria parasitica Fomme1_27083 Crypa2_343514 Fomme1_80051 Cryptodiaporthe populea Fomme1_80204 Crypo1_327771 Fomme1_80444 Crypo1_328559 Fomme1_82079 Crypo1_335598 Fomme1_82792 Crypo1_345542 Fomme1_82811 Crypo1_376330 Fomme1_89798 Crypo1_381328 Fomme1_91806 Crypo1_381563 Fomme1_95393 Crypo1_432491 Fomme1_97061 Crypo1_443797 Fomitopsis pinicola Crypo1_472123 Fompi3_1017321 Cucurbitaria berberidis Fompi3_1017322 Cucbe1_280026 Fompi3_1023716 Daldinia eschscholzii Fompi3_1034271 Da1EC12_1_12539 Fompi3_110513 Da1EC12_1_17536 Fompi3_1118553 Da1EC12_1_24646 Fompi3_1118777 Da1EC12_1_24764 Fompi3_1120393 Da1EC12_1_25458 Fompi3_1137037 Da1EC12_1_70183 Fompi3_88169 Decorospora gaudefroyi Galerina marginata Decga1_179458 Galma_104215 Delphinella strobiligena Galma_1278404 Delst1_202989 Galma_1352301 Delst1_230429 Galma_137032 Delst1_365307 Galma_143861 Diaporthe ampelina Galma_222029 Diaam1_7440 Galma_223690 Diaam1_7814 Galma_225678 Diaam1_8586 Galma_229201 Didymella zeae-maydis Galma_245845 Didma1_13214 Galma_266794 Didymocrea sadasivanii Galma_62552 Didsa1_432338 Galma_63553 Didsa1_459411 Galma_63556 Diplodia seriata Galma_72334 Dipse1_2018 Galma_72397 Dissoconium aciculare Galma_78470 Disac1_349444 Ganoderma sp. Dothidotthia symphoricarpi Gansp1_106195 Dotsy1_400389 Gansp1_115598 Endocarpon pusillum Gansp1_116882 EndpusZ1_8494 Gansp1_118798 EndpusZ1_8851 Gansp1_119170 Entoleuca mammata Gansp1_126698 Entma1_245693 Gansp1_143866 Entma1_278690 Gansp1_147418 Entma1_396117 Gansp1_151250 Entma1_410097 Gansp1_151266 Eutypa lata Gansp1_151299 Eutla1_2536 Gansp1_155853 Eutla1_3565 Gansp1_164758 Eutla1_5251 Gansp1_166943 Exophiala aquamarina Gansp1_41036 Exoaq1_8751 Gansp1_57109 Fonsecaea pedrosoi Gansp1_57679 Fonpe1_8054 Gansp1_58158 Fusarium fujikuroi Gansp1_58881 Ffsc4 Gansp1_81688 Ffsc6 Gansp1_85736 Fusfu1_1126 Gloeophyllum trabeum Fusfu1_11322 Glotr1_1_103889 Fusfu1_14268 Glotr1_1_116237 Fusfu1_2062 Glotr1_1_117331 Fusfu1_6471 Glotr1_1_131990 STC3 Glotr1_1_47645 STC5 Glotr1_1_48290 Fusarium graminearum Glotr1_1_64172 CLM1 Glotr1_1_78472 Fusgr1_10122 Glotr1_1_79917 Fusgr1_13217 Glotr1_1_80390 Fusgr1_2052 Grifola frondosa Fusgr1_4586 COP3_0_A0H81_12697 Fusgr1_548 COP3_1_A0H81_08013 Fusarium oxysporum COP3_2_A0H81_10954 Fusox2_10433 COP3_5_A0H81_08017 Fusox2_10434 COP4_0_A0H81_07725 Fusox2_10435 COP4_1_A0H81_07728 Fusox2_10673 Gymnopus luxurians Fusox2_10675 Gymlu1_1012408 Fusox2_8564 Gymlu1_1024248 Fusarium sporotrichioides Gymlu1_152409 FsTDS Gymlu1_164402 Fusarium verticillioides Gymlu1_179557 Fusve2_12377 Gymlu1_181084 Fusve2_1423 Gymlu1_239618 Fusve2_19 Gymlu1_240529 Fusve2_20 Gymlu1_242070 Fusve2_8588 Gymlu1_249731 Fusve2_8699 Gymlu1_249732 Glomerella acutata Gymlu1_257858 Gloac1_1349405 Gymlu1_266288 Gloac1_1383433 Gymlu1_474275 Gloac1_1413417 Gymlu1_70394 Gloac1_1624359 Gymlu1_74039 Gloac1_1638878 Gymlu1_775187 Glomerella cingulata Hebeloma cylindrosporum Gloci1_1722638 M413_27416 Gloci1_1750922 M413_32803 Gloci1_1755285 M413_415200 Gloci1_1819074 M413_443011 Gloci1_1825757 M413_7659 Gloci1_1830608 M413_83524 Gloci1_1835014 Heterobasidion annosum Gloci1_1852737 Hetan2_115814 Glonium stellatum Hetan2_148791 Glost2_424907 Hetan2_167573 Gremmeniella abietina Hetan2_169607 Greab1_510385 Hetan2_172256 Greab1_510929 Hetan2_181194 Grosmannia clavigera Hetan2_34201 CMQ_352 Hetan2_382802 Groc11_2976 Hetan2_382866 Groc11_8310 Hetan2_42859 Gymnascella aurantiaca Hetan2_446121 Gymau1_124723 Hetan2_454193 Gymau1_163306 Hetan2_458479 Gymnascella citrina Hetan2_48772 Gymci1_1_287288 Hetan2_51706 Gyromitra esculenta Hydnomerulius pinastri Gyresc1_452646 HYDPI_175348 Gyresc1_614921 HYDPI_90513 HirsuteIla minnesotensis HYDPI_93448 HIM_03781 HYDPI_95823 Hymenoscyphus varicosporoides Hypholoma sublateritium Hymvar1_186372 HYPSU_151315 Hymvar1_433677 Hypsu1_138166 Hymvar1_527573 Hypsu1_138665 Hymvar1_530070 Hypsu1_148365 Hymvar1_530714 Hypsu1_148385 Hypoxylon sp. Hypsu1_159396 Hyp1 Hypsu1_202683 Hyp2 Hypsu1_205915 Hyp3 Hypsu1_36467 Hyp4 Hypsu1_47068 Hyp5 Hypsu1_80866 HypCI4A_1_20984 Hypsu1_92421 HypCI4A_1_216497 Hypsizygus marmoreus HypCI4A_1_322581 COP3_1_Hypma_09878 HypCI4A_1_59230 COP3_2_Hypma_09820 HypCI4A_1_6706 COP4_Hypma_01074 HypCI4A_1_69724 Jaapia argillacea HypCI4A_1_7067 Jaaar1_125196 HypCO275_1_269219 Jaaar1_129042 HypCO275_1_31178 Jaaar1_162104 HypCO275_1_392541 Jaaar1_191378 HypCO275_1_397991 Jaaar1_192672 HypEC38_3_102477 Jaaar1_206626 HypEC38_3_372695 Jaaar1_35337 HypEC38_3_409185 Jaaar1_453389 HypEC38_3_424147 Jaaar1_47108 HypEC38_3_436214 Jaaar1_487951 Ilyonectria robusta Jaaar1_62046 Ilyrob1_438077 Laccaria amethystina Ilyrob1_458205 K443_108732 Ilyrob1_462532 K443_126876 Ilyonectria sp. K443_309839 Ilysp1_1486196 K443_619353 Ilysp1_1873426 K443_681798 Kalaharituber pfeilii K443_99583 Kalpfe1_784829 Laccaria bicolor Kalpfe1_789340 LACBI_312850 Karstenula rhodostoma LACBI_326872 Karrh1_427857 Lacbi1_297082 Karrh1_478359 Lacbi1_307420 Khuskia oryzae Lacbi1_307559 Khuory1_125966 Lacbi1_307631 Khuory1_156064 Lacbi1_308775 Khuory1_357319 Lacbi1_310816 Khuory1_456225 Lacbi1_327169 Khuory1_483548 Lacbi1_331339 Khuory1_495123 Lacbi1_333748 Lecythophora sp. Laetiporus sulphureus LecAK0013_1_225655 LAESU_64487 LecAK0013_1_337743 LAESU_657286 LecAK0013_1_358472 LAESU_657700 Lentithecium fluviatile LAESU_682207 Lenfl1_319520 LAESU_706375 Leptodontium sp. LAESU_724692 Leptod1_444196 LAESU_736295 Leptod1_455689 LAESU_739029 Leptod1_476038 LAESU_754774 Leptosphaeria maculans LAESU_760769 Lepmu1_308 LAESU_760772 Lindgomyces ingoldianus LAESU_97217 Linin1_380217 Lentinula edodes Lobaria pulmonaria LENED_000675 Lobpul1_1077425 LENED_009785 Lobpul1_1081061 LENED_011156 Lobpul1_1086700 Leucoagaricus sp. Lobpul1_1088690 AN958_00679 Lobpul1_1160659 AN958_01976 Lobpul1_1160823 AN958_05697 Lobpul1_1187714 AN958_05837 Lobpul1_1189558 AN958_08196 Lobpul1_1267101 AN958_09576 Lobpul1_1326505 AN958_09577 Lophiotrema nucula AN958_11218 Lopnu1_203111 AN958_11219 Lopnu1_576877 AN958_12529 Lopnu1_603805 Moniliophthora perniciosa Lophium mytilinum MPER_03050 Lopmy1_551480 Moniliophthora roreri Loramyces juncicola Moror_10387 Lorju1_472231 Moror_10832 Lorju1_513685 Moror_11443 Loramyces macrosporus Moror_14186 Lorma1_320020 Moror_15644 Lorma1_437337 Moror_4213 Lorma1_614065 WG66_11919 Macrophomina phaseolina WG66_12445 Macph1_8897 WG66_17918 Macroventuria anomochaeta WG66_18074 Macan1_446477 WG66_18690 Magnaporthe grisea WG66_18985 Maggr1_110458 WG66_354 Maggr1_111240 WG66_8033 Mariannaea sp. Mycena chlorophos MarPMI226_411544 MCHLO_03985 Marssonina brunnea MCHLO_05513 Marbr1_4753 MCHLO_07787 Massariosphaeria phaeospora MCHLO_08688 Masph1_606827 MCHLO_13355 Melanconium sp. Neolentinus lepideus Melsp1_127340 NEOLE_1114180 Melsp1_95914 NEOLE_1127484 Melanomma pulvis-pyrius NEOLE_1129527 Melpu1_277550 NEOLE_1133313 Melpu1_347683 NEOLE_1153406 Melanospora tiffanyae NEOLE_1157631 Melti1_461564 NEOLE_1157743 Meliniomyces bicolor NEOLE_1180214 Me1bi2_645837 NEOLE_1181640 Meliniomyces variabilis NEOLE_134104 Melva1_455976 NEOLE_318499 Metarhizium robertsii NEOLE_467896 Metro1_2405 NEOLE_632413 Metro1_3595 Omphalotus olearius Metro1_6916 Omp1 Metro1_9225 Omp10 Microdochium bolleyi Omp2 Micbo1_128564 Omp3 Micbo1_13978 Omp4 Micbo1_151202 Omp5a Micbo1_158522 Omp5b Micbo1_181072 Omp6 Micbo1_186092 Omp7 Microdochium trichocladiopsis Omp8 Mictri1_125659 Omp9 Mictri1_260337 Ophiostoma piceae Mictri1_335184 F503_01342 Mictri1_375638 Ophpic1_6625 Mictri1_422579 Paxillus involutus Microsporum canis Paxin1_101514 Micca1_2230 Paxin1_12806 Myrothecium inundatum Paxin1_137577 Myrin1_398933 Paxin1_167348 Myrin1_546039 Paxin1_176239 Nectria haematococca Paxin1_180528 Necha2_74943 Paxin1_181593 Neofusicoccum parvum Paxin1_18633 Neopa1_3315 Paxin1_77896 Neopa1_4144 Paxin1_83937 Neopa1_7973 Paxin1_86018 Neosartorya fischeri Paxillus rubicundulus Neofi1_2116 PAXRU_23853 Niesslia exilis PAXRU_642577 Nieex1_76034 Peniophora sp. Oidiodendron maius PENSP_572785 OIDMA_107833 PENSP_601208 Oidma1_107833 PENSP_625629 Ophiobolus disseminans PENSP_626963 Ophdi1_289928 PENSP_636110 Ophdi1_418300 PENSP_682634 Ophdi1_58500 PENSP_706592 Ophiostoma novo-ulmi PENSP_749173 Ophnu1_1985851 PENSP_755041 Paracoccidioides brasiliensis Phanerochaete chrysosporium Parbr1_1519 Phaca1_125341 Parbra1_1841 Phaca1_139052 Paraconiothyrium sporulosum Phaca1_197990 Parsp1_1201140 Phaca1_211240 Parsp1_1217178 Phaca1_211244 Penicillium bilaiae Phaca1_211256 Penbi1_460541 Phaca1_211257 Penicillium brevicompactum Phaca1_251936 Penbr2_53488 Phaca1_259972 Penicillium canescens Phaca1_89483 Penca1_224374 Phlebia brevispora Penicillium chrysogenum Phchr1_1815 Pench1_25529 Phchr1_3165 Pench1_6764 Phchr1_3229 PenchWisc1_1_144631 Phchr1_4239 Penicillium digitatum Phchr1_4445 Pendi1_59 Phlbr1_146388 Pendi1_8028 Phlbr1_146389 Penicillium expansum Phlbr1_148542 Penex1_331919 Phlbr1_152186 Penex1_423287 Phlbr1_153007 Penicillium janthinellum Phlbr1_18034 Penja1_454093 Phlbr1_27358 Penicillium lanosocoeruleum Phlbr1_71918 Penla1_395992 Phlbr1_75447 Penicillium oxalicum Phlbr1_83077 Penox1_1709 Phlbr1_89160 Penicillium roqueforti Phlebia centrifuga PrARS PHLCEN_10709 Penicillium thymicola PHLCEN_10849 Penth1_227129 PHLCEN_10850 Periconia macrospinosa Phlebiopsis gigantea Perma1_640487 Phlgi1_103744 Perma1_643878 Phlgi1_114823 Perma1_662832 Phlgi1_12454 Perma1_709192 Phlgi1_126738 Pestalotiopsis fici Phlgi1_157711 PFICI_04870 Phlgi1_359064 Phaeosphaeriaceae sp. Phlgi1_367715 PhaPMI808_630607 Phlgi1_80906 PhaPMI808_701240 Piloderma croceum PhaPMI808_718099 Pilcr_14594 Phialocephala scopiformis Pilcr_779936 LY89_757172 Pilcr_810716 Phisc1_722991 Pilcr_81088 Phisc1_731760 Pilcr_825684 Phisc1_779859 Pilcr_828668 Phialocephala subalpina Pilcr_98986 PAC_01018 Pisolithus microcarpus Phoma tracheiphila PISMI_111694 Photr1_393361 PISMI_546554 Phyllosticta capitalensis PISMI_636097 Phycap1_294755 PISMI_642487 Phycap1_350841 PISMI_88043 Phyllosticta citriasiana Pisolithus tinctorius Phycit1_361908 M404_137874 Phyllosticta citribraziliensis M404_170039 Phcit1_228662 M404_29719 Phcit1_230456 M404_471194 Phyllosticta citricarpa Pleurotus ostreatus Phycitr1_625980 PleosPC15_2_1039734 Phyllosticta sp. PleosPC15_2_1041418 Phy27169_293752 PleosPC15_2_1046456 Phy27169_350519 PleosPC15_2_1047596 Phycpc1_413892 PleosPC15_2_1048495 Phycpc1_489935 PleosPC15_2_1060726 Plectania melastoma PleosPC15_2_1061909 Plemel1_334852 PleosPC15_2_1073415 Plemel1_353228 PleosPC15_2_1098067 Plemel1_396069 PleosPC15_2_1106708_ Plemel1_527840 PleosPC15_2_155013 Plemel1_530055 PleosPC15_2_160242 Plemel1_533333 PleosPC15_2_161354 Plectosphaerella cucumerina PleosPC15_2_30147 Plecu1_445621 PleosPC15_2_50572 Pleomassaria siparia Plicaturopsis crispa Plesi1_495074 PLICR_119075 Podospora anserina Polyporus brumalis Podan2_5388 TPS Podan2_5672 Postia placenta Podospora curvicolla POSPL_38764 Podcur1_279887 Pospl1_101754 Podcur1_310174 Pospl1_105496 Podcur1_326203 Pospl1_106438 Podcur1_408089 Pospl1_106440 Pseudographis elatina Pospl1_125960 Pseel1_2508 Pospl1_125961 Pseudomassariella vexata Pospl1_128412 Pseve2_338773 Pospl1_130417 Pseve2_344074 Pospl1_24705 Pseve2_354204 Pospl1_44163 Pseudovirgaria hyperparasitica Pospl1_45581 Psehy1_445678 Pospl1_46699 Psehy1_496475 Pospl1_59374 Purpureocillium sp. Pospl1_60326 Pursp1_260473 Pospl1_87954 Pursp1_363397 Pospl1_89105 Pyrenochaeta sp. Pospl1_91093 Pyrsp1_595056 Pospl1_92799 Rhizoscyphus ericae Pospl1_95481 Rhier1_616313 Pospl1_97252 Rhier1_704713 Pospl1_98072 Rhytidhysteron rufulum Pospl1_99496 Rhyru1_1_114183 Punctularia strigosozonata Rhyru1_1_114682 Punst1_108886 Rhyru1_1_116218 Punst1_134752 Sarcoscypha coccinea Punst1_135766 Sarco1_413089 Punst1_136240 Sarco1_477087 Punst1_138799 Sarco1_533689 Punst1_146877 Septoria musiva Punst1_45005 Sepmu1_150980 Punst1_61346 Sepmu1_51031 Punst1_62271 Septoria populicola Punst1_69007 Seppo1_112324 Punst1_69869 Seppo1_36729 Pycnoporus cinnabarinus Setosphaeria turcica BN946_scf184637.g2 Settu1_155455 BN946_scf184747.g24 Sporothrix brasiliensis BN946_scf184790.g3 SPBR_04258 BN946_scf184934.g16 Sporothrix schenckii BN946_scf184940.g8 HMPREF1624_08272 BN946_scf184945.g13 Stagonospora nodorum BN946_scf184945.g9 Stano2_10081 Rhizoctonia solani Stano2_10963 RSOL_092870 Stagonospora sp. RSOL_312180 Stasp1_218798 RSOL_403460 Stasp1_378012 RSOL_403680 Symbiotaphrina kochii RSOL_510110 Symko1_913078 RSOLAG22IIIB_02130 Talaromyces marneffei RSOLAG22IIIB_06073 Talma1_2_9490 RSOLAG22IIIB_08057 Talaromyces proteolyticus RSOLAG22IIIB_09566 Talpro1_398870 RSOLAG22IIIB_09570 Talaromyces stipitatus RSOLAG22IIIB_09739 Talst1_2_11311 V565_056500 Teratosphaeria nubilosa V565_214290 Ternu1_346415 Rhizopogon vesiculosus Thielavia antarctica AZE42_03256 Thian1_441220 AZE42_03257 Thielavia appendiculata AZE42_03950 Thiap1_653559 AZE42_04671 Thielavia arenaria AZE42_04965 Thiar1_832266 AZE42_07544 Thielavia terrestris AZE42_08339 Thite2_2110120 AZE42_08340 Thozetella sp. AZE42_08772 ThoPMI491_1_727832 AZE42_08877 Trematosphaeria pertusa AZE42_10031 Trepe1_605244 AZE42_10033 Trichoderma asperellum AZE42_12242 Trias1_142130 Rhizopogon vinicolor Trias1_53311 K503_537004 Triasp1_109551 K503_537037 Triasp1_373402 K503_696597 Triasp1_382539 K503_699336 Trichoderma atroviride K503_740792 Triat2_210728 K503_767681 Triat2_321366 K503_783219 Triat2_86577 K503_790659 Trichoderma citrinoviride K503_791387 Trici4_1108149 K503_849799 Trici4_66121 Schizophyllum commune Trichoderma guizhouense Schco1_15679 A0O28_0096870 Schco1_17515 Trichoderma harzianum Schco1_55597 THAR02_10331 Schizopora paradoxa Triha1_502236 SCHPA_385230 Triha1_523651 SCHPA_600612 Triha1_74633 SCHPA_600636 Trihar1_48270 SCHPA_626535 Trihar1_691238 SCHPA_825685 Trihar1_819783 SCHPA_828532 Trihar1_844963 SCHPA_828604 Trichoderma longibrachiatum SCHPA_890331 Trilo3_1442452 SCHPA_893708 Trilo3_1456582 SCHPA_894889 Trichoderma reesei SCHPA_910670 Trire2_112028 SCHPA_931668 Trire2_59597 SCHPA_938296 Trire2_68401 SCHPA_940716 TrireRUTC30_1_12695 SCHPA_940718 TrireRUTC30_1_75235 SCHPA_940719 Trichoderma virens SCHPA_943858 TriviGv29_8_2_187786 SCHPA_944256 TriviGv29_8_2_222187 Scleroderma citrinum TriviGv29_8_2_41289 SCLCI_100351 Trichophaea hybrida SCLCI_1207283 Trihyb1_876524 SCLCI_12509 Trichophyton rubrum SCLCI_134791 Triru1_8324 Serendipita indica Trichophyton verrucosum PIIN_06735 Triver1_4178 Serendipita vermifera Trypethelium eluteriae M408_327964 Tryvi1_496934 Serpula lacrymans Usnea florida cyc6_SERLA_441878 Usnflo1_55552 SerlaS7_3_2_108414 Usnflo1_574162 SerlaS7_3_2_108585 Usnflo1_877966 SerlaS7_3_2_165924 Usnflo1_901038 SerlaS7_3_2_175395 Usnflo1_955721 SerlaS7_3_2_187364 Venturia pirina SerlaS7_3_2_61540 Venpi1_211509 SerlaS7_3_2_90456 Venpi1_218661 SerlaS7_3_2_94439 Wilcoxina mikolae Sistotremastrum niveocremeum Wilmi1_425792 SISNI_412344 Xylaria hypoxylon SISNI_413094 Xylhyp1_472420 SISNI_417792 Xylhyp1_503745 SISNI_419019 Xylhyp1_529710 SISNI_419037 Xylhyp1_540106 SISNI_420386 Xylhyp1_540898 SISNI_437403 Xylhyp1_549956 SISNI_445623 Xylhyp1_569642 SISNI_446492 Xylhyp1_576955 SISNI_455901 Xylhyp1_588565 SISNI_475911 Xylhyp1_614361 SISNI_482322 Xylariales sp. SISNI_486677 XylPMI506_151792 SISNI_490653 Xy1PMI506_435412 SISNI_511593 Xy1PMI506_469434 SISNI_511679 Xy1PMI506_473008 SISNI_534675 XylPMI506_478051 Sistotremastrum suecicum Zymoseptoria ardabiliae SISSU_1009262 Zymar1_773224 SISSU_1027225 Zymoseptoria pseudotritici SISSU_1035907 Zymps1_798041 SISSU_1035914 SISSU_1052084 SISSU_1061476 SISSU_1062338 SISSU_1062347 SISSU_1065756 SISSU_1067234 SISSU_1069491 SISSU_1132250 SISSU_138780 SISSU_221655 SISSU_992550 SISSU_993764 Sphaerobolus stellatus Sphst_181402 Sphst_184320 Sphst_192154 Sphst_255906 Sphst_255948 Sphst_266313 Sphst_266350 Sphst_47084 Sphst_55620 Sphst_68403 Sphst_785590 Stereum hirsutum STEHI_69906 Stehi1_111121 Stehi1_128017 Stehi1_146390 Stehi1_155443 Stehi1_159379 Stehi1_161672 Stehi1_167646 Stehi1_25180 Stehi1_45387 Stehi1_50042 Stehi1_52743 Stehi1_64702 Stehi1_70268 Stehi1_73029 Suillus luteus CY34_184278 CY34_23707 CY34_71869 CY34_799377 CY34_801563 CY34_80413 CY34_81655 Termitomyces sp. J132_01558 J132_02641 J132_04009 J132_04469 J132_04694 J132_04698 J132_05842 J132_07850 J132_08389 J132_09198 J132_09201 J132_09437 J132_09567 J132_09570 J132_09647 J132_09686 J132_09687 J132_10181 J132_11041 Thanatephorus cucumeris BN14_00857 BN14_03718 RSOLAG1IB_02393 RSOLAG1IB_05967 RSOLAG1IB_05988 RSOLAG1IB_06038 Trametes pubescens TRAPUB_14195 TRAPUB_4416 TRAPUB_4417 TRAPUB_6039 TRAPUB_6042 TRAPUB_7379 TRAPUB_9141 Trametes versicolor Trave1_118176 Trave1_119121 Trave1_122204 Trave1_124930 Trave1_125681 Trave1_167198 Trave1_169091 Trave1_20994 Trave1_30977 Trave1_35003 Trave1_44143 Trave1_47002 Trave1_47003 Trave1_47026 Trave1_75578 Tulasnella calospora M407_214286 M407_214353 M407_49795 M407_51027 M407_66752 M407_70959 M407_78466 Wolfiporia cocos Wolco1_117435 Wolco1_120409 Wolco1_133798 Wolco1_134393 Wolco1_145847 Wolco1_150507 Wolco1_15395 Wolco1_162429 Wolco1_61127 Wolco1_62102 Wolco1_63709 Wolco1_70381 Wolco1_72514 Wolco1_72849 Wolco1_89832 Wolco1_95045 Wolco1_95361

With the 1408 TPSs, a phylogenetic tree which has seven major distinct TPS clades (FIG. 18) was built and all-by-all BLAST analysis with enzyme function initiative (EFI)-enzyme similarity tool (EST) (FIG. 19) was carried out. All the clades have at least two characterized TPS enzymes. The promiscuous TPSs producing a series of muurolene and cadinene compounds (such as Omp1-3, Cop1-3, AAE3_13190 and AAE3_6595) clustered together in clade I (FIG. 18). Interestingly, all of the characterized TPS in clade I catalysed 1,10 cyclization of FPP (FIG. 17). All the eight characterized Δ6-protoilludene (1,11 cyclization of FPP, FIG. 17) synthases, together with other 32 putative TPSs, closely grouped in clade II. In addition, the four TPSs AAE3_9008, AAE3_6743, AAE3_0444, AAE3_5024 segmented closely in clade II, with multiple products including muurolene and cadinene (1,10 cyclization of FPP, FIG. 17). TPSs with cadinene as the major product (Cop4, Stehi1_128017, Omp4-5a,b and AAE3_9164) clustered together in clade III. Viridiflorene and viridiflorol synthases (AAE3_12839 and AAE3_13291, 1,11 cyclization of FPP, FIG. 17) were also in clade III but were distinct from cadiene synthases. Hyp1, 2 and 5 scattered loosely in clade IV as they have different products and different catalytic mechanisms. Hyp1 produces a linear terpene nerolidol, but Hyp2 and Hyp5 catalyze cadinene and bulnesene, respectively (1,10 cyclization of FPP). Ffsc4 (koraiol, 1,11 cyclization) and some TPSs responsible for 1,6 or 1,7 cyclization of FPP (Omp8-10, Cop6 and FsTDS (trichodiene)) clustered in clade V. Moreover, Hyp4 (unknown sesquiterpene products) and the monoterpene synthase Hyp3 (1,8-cineole) segmented in clade V. In clade VI, only two aristolochene (1,10 cyclization of FPP) synthases (AtARS (Cane and Kang, 2000) and PrARS (Hohn and Plattner, 1989)) were characterized. Lastly, a few characterized TPSs with different cyclization mechanisms, including STC3 ((+)-eremophilene, 1,10 cyclization of FPP), STC5 ((−)-guaia-6,10(14)-diene, 1,10 cyclization of FPP), BcBOT2 (presilphiperfolan-8β-ol, 1,11 cyclization of FPP) and Ffsc6 ((−)-a-acorenol, 1,6 cyclization of FPP), scattered in clade VII. In sum, most of Basidiomycota TPSs (including all the 11 A. aegerita TPSs) grouped in clade I, II and III but Ascomycota TPSs mainly scattered in clade IV, V, VI and VII. Badisomycota TPSs, especially closely clustered ones, in each clade often share the similar cyclization mechanism. In contrast, Ascomycota TPSs in the same clade could have diverse cyclization mechanisms.

EXAMPLE 6

Predictive Framework to Uncover Other Fungal Viridiflorol Synthases

Knowledge acquired by studying the TPS products and the sequence conservation in each distinct clade provides a valuable basis for mechanistic understanding of the distinct activities. And it could be used to engineer and design more effective enzymes and to probe and even predict the functions of unknown TPSs. To test the predictive capability of the framework, identification of viridiflorol synthases in other species was carries out. The reason viridiflorol synthase was chosen is that there is only one type of plant viridiflorol synthase reported among all kinds of species. Analyzed by the phylogenetic tree in FIG. 18 and all-by-all BLAST in FIG. 19, 15 fungal TPS homologs were closely clustered. Four of them (Sphst_47084 from Sphaerobolus stellatus, Denbi1_816208 from Dendrothele bispora, Galma_104215 from Galerina marginata and Pilcr_825684 from Piloderma croceum) were recombinantly expressed in E. coli and their products were analysed. The TPSs highlighted with circle (“●”) were characterized in this study. Among them, four TPSs (Sphst_47084 from Sphaerobolus stellatus, Denbi1_816208 from Dendrothele bispora, Galma_104215 from Galerina marginata and Pilcr_825684 from Piloderma croceum) were cloned and expressed in the chassis strain. The E. coli culture expressing Sphst_47084 and Denbi1_816208, the most closely related to AAE3_13291, produced identical products as AAE3_13291, viridiflorol 7 (-90%) and viridiflorene 6 (-10%) (FIG. 24). Interestingly, the main product of Galma_104215 was tentatively identified as β-gurjunene, a compound structurally similar to viridiflorene (FIG. 24). However, the cells expressing Pilcr_825684 produced γ-cadinene as the main product and a few minor sesquiterpenes including viridiflorene.

-   The results support that the phylogenetic tree could be used for     identification of novel TPSs with similar functions.

EXAMPLE 7

Prediction and Validation of Fungal Linalool and Nerolidol Synthases (LNSs)

Starting with the sequence of AAE3_9435, identification of other NLSs in different fungal species was obtained by a BLAST search in databases of the Joint Genome Institute (JGI, http://jgi.doe.gov/fungi) and Universal Protein Resource (UniProt, http://www.uniprot.org/). EFI-EST analysis was carried out and a group of TPS homologues were shown to be clustered with AAE3_9435. By setting the alignment score to between 80 and 90, a smaller set of candidates were selected. With the selected cluster of TPSs in FIG. 20. A focused alignment indicated that 11 fungal TPSs were clustered closely with AAE3_9435 including two other TPSs from Agrocybe aegerita, AAE3_05024 and AAE3_04444 (SEQ ID NO: 27), three from Agrocybe pediades (Agrped1_689671 (SEQ ID NO: 2), Agrped1_689675 (SEQ ID NO: 3), Agrped1_820868), three from Galerina marginata (Galma_223690 (SEQ ID NO: 4), Galma_266794 (SEQ ID NO: 77), Galma_63556), two from Hypholoma sublateritium (Hypsu1_148365, Hypsu1_148385(SEQ ID NO: 5)) and M413_27416 from Hebeloma cylindrosporum (FIG. 20). Characterized in our previous study, AAE3_05024, the most closely related TPS to AAE3_9435, seems to be a pseudogene. The main products of AAE3_04444 were γ-muurolene (33%) and β-cadinene (21%). The other TPSs in FIG. 21 have not been functionally annotated. As a proof of concept, five out of the nine uncharacterized TPSs were chosen to test their functions. All five TPSs give rise to at least one terpene when expressed in the E. coli strain overproducing IPP and DMAPP. In E. coli strains expressing Agrped1_689675 only linalool was found in the headspace of the culture. Similar to AAE3_9435, Agrped1_689671, Galma_223690 and Hypsu1_148385 showed a bifunctional NLS function producing nerolidol and linalool (FIG. 21B). Galma_266794 clones leaded to the sesquiterpene germacrene D (62%, validated by Cubeb essential oil) as main product and a few other sesquiterpenes including δ-cadinene (17%), γ-muurolene (8%), but no monoterpene. Due to the lack of the GPP synthase in the E. coli strain, the concentration of intracellular FPP was much higher than that of intracellular GPP. Consequently, all the four TPSs (AAE3_9435, Agrped1_689671, Galma_223690 and Hypsu1_148385) produced nerolidol as the main product (88-96%) and linalool as the minor product (2-10%, FIG. 21). However, when expressed in the same E. coli strain, Agrped1_689675 produced only linalool but no sesquiterpenes. The data indicated that Agrped1_689675, is an exclusive monoterpene synthase and has no activity of sesquiterpene synthase thus this was named as ‘Ape_LS’. Interestingly, despite with different products, all the six TPSs shared some very conserved regions in the metal-binding motif (such as ‘DEYTD’ and ‘NDMHSYxxE’ region). FIG. 25 shows the conserved regions for sesquiterpene and monoterpene synthases. The 2 conserved domains are DD(E/N/Y/S)XXD and NDSE. The two conserved domains served as an important pre-screening of terpene synthase homologues. Those homologues missing or having incomplete domains often have no activities and thus are excluded in our screening process.

EXAMPLE 8

Mutating the LS for a Different Function

As an exclusive monoterpene synthase, it was hypothesized that a point mutation of Agrped1_689675 (SEQ ID NO: 3) could change its function and products. To test this hypothesis, a few positions where Agrped1_689675 and the rest are different were highlighted (FIG. 22). The crystal structure in FIG. 26 was used to guide the engineering of Agrped_689675. Among different amino acids, F204 was chosen as the first to mutate. It was found that 3 out of 6 mutants (F204D, F204G and F204R) had different product profiles. Unlike wild type produces only linalool, they produced both geranyl acetate (predicted by NIST library) and linalool (FIG. 23) while the other three mutants (F204I, F204L and F204V) had no significant effects on enzyme activity and functions. More interestingly, the production of geranyl acetate is inversely correlated with that of linalool (FIG. 23C).

The homologue model of Agr1 (Agrped1_689675) and Agr3 (Agrped1_689671) was built based on the structure of 1,8-cineole synthase from Streptomyces clavuligerus (PDB ID: 5nx5, 5nx6). The binding pocket, consisting of 15 residues within 6 Å from the substrate, was determined by PyMOL software v2.1.1 and highlighted here. The models were used to guide and understand the mutation of linalool/nerolidol synthases for improved selectivity or change of selectivity.

A summary of the sequence listing can be found in Table 5.

TABLE 5 Summary of sequence listing. Name Description SEQ ID NO AAE3_109435 Amino acid sequence of wild type 1 Agrocybe aegerita FTPS Agrped1_689671 Amino acid sequence of wild type 2 Agrocybe pediades FTPS Agrped1_689675 Amino acid sequence of wild type 3 Agrocybe pediades FTPS Galma_223690 Amino acid sequence of wild type 4 Galerina marginata FTPS Hypsu_148385 Amino acid sequence of wild type 5 Hypholoma sublateritium FTPS Ec.dxs Amino acid sequence of wild type 6 Escherichia coli DXS Agrped1_689675_mut1  Amino acid sequence of genetically modified 7 Agrped1_689675, C-terminal truncation Agrped1_689675_mut2  Amino acid sequence of genetically modified 8 Agrped1_689675, C-terminal truncation Agrped1_689675_mut3  Amino acid sequence of genetically modified 9 Agrped1_689675, C-terminal truncation Agrped1_689675_mut4  Amino acid sequence of genetically modified 10 Agrped1_689675, N-terminal truncation Agrped1_689675_mut5  Amino acid sequence of genetically modified 11 Agrped1_689675, N-terminal truncation Agrped1_689675_mut6  Amino acid sequence of genetically modified 12 Agrped1_689675, F204G Agrped1_689675_mut7  Amino acid sequence of genetically modified 13 Agrped1_689675, F204V Agrped1_689675_mut8  Amino acid sequence of genetically modified 14 Agrped1_689675, F2041 Agrped1_689675_mut9  Amino acid sequence of genetically modified 15 Agrped1_689675, F204D Agrped1_689675_mut10 Amino acid sequence of genetically modified 16 Agrped1_689675, F204L Agrped1_689675_mut11 Amino acid sequence of genetically modified 17 Agrped1_689675, F204R Agrped1_689675_mut12 Amino acid sequence of genetically modified 18 Agrped1_689675, 1UP-3DW Agrped1_689675_mut13 Amino acid sequence of genetically modified 19 Agrped1_689675, 3UP-1DW AAE3_109435_mut1 Amino acid sequence of genetically modified 20 AAE3_109435, C-terminal truncation Agrped1_689671_mut1 Amino acid sequence of genetically modified 21 Agrped1_689671, C-terminal truncation Galma_223690_mut 1 Amino acid sequence of genetically modified 22 Galma_223690, C-terminal truncation Hypsu_148385_mut1 Amino acid sequence of genetically modified 23 Hypsu_148385, C-terminal truncation Ec.dxs_SL3 Amino acid sequence of genetically 24 modified E. coli DXS Ec.dxs_SL5 Amino acid sequence of genetically 25 modified E. coli DXS AAE3_04120 Amino acid sequence of cDNA of wild type 26 AAE3_04120 FTPS AAE3_04444 Amino acid sequence of cDNA of wild type 27 AAE3_04444 FTPS AAE3_06595 Amino acid sequence of cDNA of wild type 28 AAE3_06595 FTPS AAE3_06743 Amino acid sequence of cDNA of wild type 29 AAE3_06743 FTPS AAE3_09164 Amino acid sequence of cDNA of wild type 30 AAE3_09164 FTPS AAE3_10454 Amino acid sequence of cDNA of wild type 31 AAE3_10454 FTPS AAE3_13291 Amino acid sequence of cDNA of wild type 32 AAE3_13291 FTPS AAE3_13190 Amino acid sequence of cDNA of wild type 33 AAE3_13190 FTPS AAE3_12839 Amino acid sequence of cDNA of wild type 34 AAE3_12839 FTPS AAE3_109435 Nucleic acid sequence of cDNA of wild type 35 AAE3_109435 FTPS Agrped1_689671 Nucleic acid sequence of cDNA of wild type 36 Agrped1_689671 FTPS Agrped1_689675 Nucleic acid sequence of cDNA of wild type 37 Agrped1_689675 FTPS Galma_223690 Nucleic acid sequence of cDNA of wild type 38 Galma_223690 FTPS Hypsu_148385 Nucleic acid sequence of cDNA of wild type 39 Hypsu_148385 FTPS AAE3_04120 Nucleic acid sequence of cDNA of wild type 40 AAE3_04120 FTPS AAE3_04444 Nucleic acid sequence of cDNA of wild type 41 AAE3_04444 FTPS AAE3_06595 Nucleic acid sequence of cDNA of wild type 42 AAE3_06595 FTPS AAE3_06743 Nucleic acid sequence of cDNA of wild type 43 AAE3_06743 FTPS AAE3_09164 Nucleic acid sequence of cDNA of wild type 44 AAE3_09164 FTPS AAE3_10454 Nucleic acid sequence of cDNA of wild type 45 AAE3_10454 FTPS AAE3_12839 Nucleic acid sequence of cDNA of wild type 46 AAE3_12839 FTPS AAE3_13190 Nucleic acid sequence of cDNA of wild type 47 AAE3_13190 FTPS AAE3_13291 Nucleic acid sequence of cDNA of wild type 48 AAE3_13291 FTPS AAE3_109435 Nucleic acid sequence of cDNA of wild type 49 AAE3_109435 FTPS Ec.dxs Nucleic acid sequence of wild 50 type Escherichia coli DXS Ec.dxs_SL3 Nucleic acid sequence of genetically 51 modified E. coli DXS Ec.dxs_SL5 Nucleic acid sequence of genetically 52 modified E. coli DXS AAE3_109435 Nucleic acid sequence of wild 53 type Agrocybe aegerita FTPS Agrped1_689671 Nucleic acid sequence of wild 54 type Agrocybe pediades FTPS Agrped1_689675 Nucleic acid sequence of wild 55 type Agrocybe pediades FTPS Galma_223690 Nucleic acid sequence of wild 56 type Galerina marginata FTPS Hypsu_148385 Nucleic acid sequence of wild 57 type Hypholoma sublateritium FTPS Agrped1_689675_mut1  Nucleic acid sequence of genetically modified 58 Agrped1_689675, C-terminal truncation Agrped1_689675_mut2  Nucleic acid sequence of genetically modified 59 Agrped1_689675, C-terminal truncation Agrped1_689675_mut3  Nucleic acid sequence of genetically modified 60 Agrped1_689675, C-terminal truncation Agrped1_689675_mut4  Nucleic acid sequence of genetically modified 61 Agrped1_689675, N-terminal truncation Agrped1_689675_mut5  Nucleic acid sequence of genetically modified 62 Agrped1_689675, N-terminal truncation Agrped1_689675_mut6  Nucleic acid sequence of genetically 63 modified Agrped1_689675, F204G Agrped1_689675_mut7  Nucleic acid sequence of genetically 64 modified Agrped1_689675, F204V Agrped1_689675_mut8  Nucleic acid sequence of genetically 65 modified Agrped1_689675, F2041 Agrped1_689675_mut9  Nucleic acid sequence of genetically 66 modified Agrped1_689675, F204D Agrped1_689675_mut10 Nucleic acid sequence of genetically 67 modified Agrped1_689675, F204L Agrped1_689675_mutl 11 Nucleic acid sequence of genetically 68 modified Agrped1_689675, F204R Agrped1_689675_mut12 Nucleic acid sequence of genetically 69 modified Agrped1_689675, 1UP-3DW Agrped1_689675_mut13 Nucleic acid sequence of genetically 70 modified Agrped1_689675, 3UP-1DW AAE3_109435_mut1 Nucleic acid sequence of genetically modified 71 AAE3_109435, C-terminal truncation Agrped1_689671_mut1 Nucleic acid sequence of genetically modified 72 Agrped1_689671, C-terminal truncation Galma_223690_mut1 Nucleic acid sequence of genetically modified 73 Galma_223690, C-terminal truncation Hypsu_148385_mut1 Nucleic acid sequence of genetically modified 74 Hypsu_148385, C-terminal truncation TPS31 Amino acid sequence of wild type 75 Solanum lycopersicum FTPS MqTPS1 Amino acid sequence of wild type 76 Melaleuca quinquenervia FTPS Galma_266794 Amino acid sequence of wild type 77 Galerina marginata FTPS Hyp3 Amino acid sequence of Hyp3 FTPS 78 Hyp5 Amino acid sequence of Hyp5 FTPS 79 Hyp2 Amino acid sequence of Hyp2 FTPS 80 Omp3 Amino acid sequence of Omp3 FTPS 81 Cop3 Amino acid sequence of Cop3 FTPS 82 Cop1 Amino acid sequence of Cop1 FTPS 83 Omp1 Amino acid sequence of Omp4 FTPS 84 Omp2 Amino acid sequence of Omp2 FTPS 85 Cop2 Amino acid sequence of Cop2 FTPS 86 Cop4 Amino acid sequence of Cop4 FTPS 87 Stehi_128017 Amino acid sequence of Stehi_128017 FTPS 88 Omp4 Amino acid sequence of Omp4 FTPS 89 Omp5a Amino acid sequence of Omp5a FTPS 90 Omp5b Amino acid sequence of Omp5b FTPS 91 AAE3_05024 Amino acid sequence of AAE3_05024 FTPS 92 AAE3_09008 Amino acid sequence of AAE3_09008 FTPS 93 AAE3_04210 Amino acid sequence of AAE3_04210 FTPS 94 Omp6 Amino acid sequence of Omp6 FTPS 95 Stehi_25180 Amino acid sequence of Stehi_25180 FTPS 96 Omp7 Amino acid sequence of Omp7 FTPS 97 Prol Amino acid sequence of Prol FTPS 98 Stehi_73029 Amino acid sequence of Stehi_73029 FTPS 99 Stehi_64702 Amino acid sequence of Stehi_64702 FTPS 100 Cop5 Amino acid sequence of Cop5 FTPS 101 Stehi_159379 Amino acid sequence of Stehi_159379 FTPS 102 Cop6 Amino acid sequence of Cop6 FTPS 103 Ompl0 Amino acid sequence of Omp10 FTPS 104 Omp9 Amino acid sequence of Omp9 FTPS 105 Omp8 Amino acid sequence of Omp8 FTPS 106 Hyp3 metal First metal binding domain 107 binding domain 1 of Hyp3 FTPS Hyp3 metal Second metal binding domain 108 binding domain 2 of Hyp3 FTPS Hyp5 metal First metal binding domain 109 binding domain 1 of Hyp5 FTPS Hpy5 metal Second metal binding domain 110 binding domain 2 of Hyp5 FTPS Hyp2 metal First metal binding domain 111 binding domain 1 of Hyp2 FTPS Hyp2 metal Second metal binding domain 112 binding domain 2 of Hyp2 FTPS Omp3 metal First metal binding domain 113 binding domain 1 of Omp3 FTPS Omp3 metal Second metal binding domain 114 binding domain 2 of Omp3 FTPS AAE3_13190 metal First metal binding domain of 115 binding domain 1 AAE3_13190 FTPS AAE3_13190 metal Second metal binding domain of 116 binding domain 2 AAE3_13190 FTPS Cop3 metal First metal binding domain 117 binding domain 1 of Cop3 FTPS Cop3 metal Second metal binding domain 118 binding domain 2 of Cop3 FTPS AAE3_06595 metal First metal binding domain of 119 binding domain 1 AAE3_06595 FTPS AAE 06595 metal Second metal binding domain of 120 binding domain 2 AAE3_06595 FTPS Cop1 metal First metal binding domain 121 binding domain 1 of Cop1 FTPS Cop1 metal Second metal binding domain 122 binding domain 2 of Cop1 FTPS Omp1 metal First metal binding domain 123 binding domain 1 of Omp1 FTPS Omp1 metal Second metal binding domain 124 binding domain 2 of Omp1 FTPS Omp2 metal First metal binding domain 125 binding domain 1 of Omp2 FTPS Omp2 metal Second metal binding domain 126 binding domain 2 of Omp2 FTPS Cop2 metal First metal binding domain 127 binding domain 1 of Cop2 FTPS Cop2 metal Second metal binding domain 128 binding domain 2 of Cop2 FTPS AAE3_12839 metal First metal binding domain of 129 binding domain 1 AAE3_12839 FTPS AAE3_12839 metal Second metal binding domain of 130 binding domain 2 AAE3_12839 FTPS AAE3_13291 metal First metal binding domain of 131 binding domain 1 AAE3_13291 FTPS AAE3_13291 metal Second metal binding domain of 132 binding domain 2 AAE3_13291 FTPS AAE3_09164 metal First metal binding domain of 133 binding domain 1 AAE3_09164 FTPS AAE3_09164 metal Second metal binding domain of 134 binding domain 2 AAE3_09164 FTPS Cop4 metal First metal binding domain 135 binding domain 1 of Cop4 FTPS Cop4 metal Second metal binding domain 136 binding domain 2 of Cop4 FTPS Stehi_128017 metal First metal binding domain of 137 binding domain 1 Stehi_128017 FTPS Stehi_128017 metal Second metal binding domain of 138 binding domain 2 Stehi_128017 FTPS Omp4 metal First metal binding domain 139 binding domain 1 of Omp4 FTPS Omp4 metal Second metal binding domain 140 binding domain 2 of Omp4 FTPS Omp5a metal First metal binding domain 141 binding domain 1 of Omp5a FTPS Omp5a metal Second metal binding domain 142 binding domain 2 of Omp5a FTPS Omp5b metal First metal binding domain 143 binding domain 1 of Omp5b FTPS Omp5b metal Second metal binding domain 144 binding domain 2 of Omp5b FTPS AAE3_04444 metal First metal binding domain of 145 binding domain 1 AAE3_04444 FTPS AAE3_04444 metal Second metal binding domain of 146 binding domain 2 AAE3_04444 FTPS AAE3_05024 metal First metal binding domain of 147 binding domain 1 AAE3_05024 FTPS AAE3_05024 metal Second metal binding domain of 148 binding domain 2 AAE3_05024 FTPS AAE3_06743 metal First metal binding domain of 149 binding domain 1 AAE3_06743 FTPS AAE3_06743 metal Second metal binding domain of 150 binding domain 2 AAE3_06743 FTPS AAE3_09008 metal First metal binding domain of 151 binding domain 1 AAE3_09008 FTPS AAE3_09008 metal Second metal binding domain of 152 binding domain 2 AAE3_09008 FTPS AAE3_10454 metal First metal binding domain of 153 binding domain 1 AAE3_10454 FTPS AAE3_10454 metal Second metal binding domain of 154 binding domain 2 AAE3_10454 FTPS AAE3_04210 metal First metal binding domain of 155 binding domain 1 AAE3_04210 FTP AAE3_04210 metal Second metal binding domain of 156 binding domain 2 AAE3_04210 FTPS Omp6 metal First metal binding domain 157 binding domain 1 of Omp6 FTPS Omp6 metal Second metal binding domain 158 binding domain 2 of Omp6 FTPS Stehi_25180 metal First metal binding domain of 159 binding domain 1 Stehi_25180 FTPS Stehi_25180 metal Second metal binding domain of 160 binding domain 2 Stehi_25180 FTPS Omp7 metal First metal binding domain 161 binding domain 1 of Omp7 FTPS Omp7 metal Second metal binding domain 162 binding domain 2 of Omp7 FTPS Pro1 metal First metal binding domain 163 binding domain 1 of Pro1 FTPS Pro1 metal Second metal binding domain 164 binding domain 2 of Pro1 FTPS Stehi_73029 metal First metal binding domain of 165 binding domain 1 Stehi_73029 FTPS Stehi_73029 metal Second metal binding domain of 166 binding domain 2 Stehi_73029 FTPS Stehi_64702 metal First metal binding domain of 167 binding domain 1 Stehi_64702 FTPS Stehi_64702 metal Second metal binding domain of 168 binding domain 2 Stehi_64702 FTPS Cop5 metal First metal binding domain 169 binding domain 1 of Cop5 FTPS Cop5 metal Second metal binding domain 170 binding domain 2 of Cop5 FTPS Stehi_159379 metal First metal binding domain of 171 binding domain 1 Stehi_159379 FTPS Stehi_159379 metal Second metal binding domain of 172 binding domain 2 Stehi_159379 FTPS Cop6 metal First metal binding domain 173 binding domain 1 of Cop6 FTPS Cop6 metal Second metal binding domain 174 binding domain 2 of Cop6 FTPS Omp10 metal First metal binding domain 175 binding domain 1 of Omp10 FTPS Omp10 metal Second metal binding domain 176 binding domain 2 of Omp10 FTPS Omp9 metal First metal binding domain 177 binding domain 1 of Omp9 FTPS Omp9 metal Second metal binding domain 178 binding domain 2 of Omp9 FTPS Omp8 metal First metal binding domain 179 binding domain 1 of Omp8 FTPS Omp8 metal Second metal binding domain 180 binding domain 2 of Omp8 FTPS

Equivalents

-   The foregoing examples are presented for the purpose of illustrating     the invention and should not be construed as imposing any limitation     on the scope of the invention. It will readily be apparent that     numerous modifications and alterations may be made to the specific     embodiments of the invention described above and illustrated in the     examples without departing from the principles underlying the     invention. All such modifications and alterations are intended to be     embraced by this application. 

1. A bacterial strain comprising one or more vectors encoding a) one or more enzymes to produce one or more terpene precursors; and b) a fungal terpene synthase (FTPS).
 2. The bacterial strain according to claim 1, wherein the one or more vectors comprise one or more nucleotide sequences encoding the one or more enzymes and the FTPS, operably linked to an inducible or consitutive promoter.
 3. The bacterial strain according to claim 1, wherein the one or more enzymes to produce the one or more terpene precursors is part of the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway, optionally wherein the enzyme is 1-deoxyxylulose-5-phosphate synthase (DXS), isopentenyl diphosphate isomerase (IDI) or both, optionally wherein the DXS comprises the amino acid sequence set forth in SEQ ID NO:
 6. 4.-5. (canceled)
 6. The bacterial strain according to claim 3, wherein the DXS is genetically modified, optionally wherein the genetically modified DXS comprises the amino acid sequence set forth in SEQ ID NO: 24 or 25, optionally wherein the DXS comprises an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to an amino acid sequence set forth in SEQ ID NO: 6, SEQ ID NO: 24 or
 25. 7.-8. (canceled)
 9. The bacterial strain according to claim 1, wherein the one or more enzymes to produce the one or more terpene precursors is expressed at an elevated level compared to a wild type enzyme, optionally wherein the one or more terpene precursors is farnesyl pyrophosphate (FPP), geranyl pyrophosphate (GPP), geranylgeranyl pyrophosphate (GGPP), or combinations thereof.
 10. (canceled)
 11. The bacterial strain according to claim 1, wherein the FTPS is a monoterpene synthase or a sesquiterpene synthase, optionally wherein the FTPS comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO: 30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, and SEQ ID NO:34, optionally wherein the FTPS comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, and SEQ ID NO:39. 12.-13. (canceled)
 14. The bacterial strain according to claim 11, wherein the FTPS is expressed at a higher level than a wild-type FTPS.
 15. The bacterial strain according to claim 1, wherein the FTPS is genetically modified, optionally wherein the genetically modified FTPS comprises an amino acid sequence selected from the group consisting of SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16 SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, and SEQ ID NO:
 23. 16. (canceled)
 17. The bacterial strain according to claim 1, wherein the FTPS comprises an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to an amino acid sequences set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16, SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33 and SEQ ID NO:
 34. 18. The bacterial strain according to claim 17, wherein the bacterial strain is Escherichia coll.
 19. A genetically modified 1-deoxyxylulose-5-phosphate synthase (DXS) enzyme, wherein the genetic modification is a mutation at one or more amino acid positions.
 20. The genetically modified DXS enzyme according to claim 19, wherein the mutation is selected from the group consisting of H105T, E210D, Q459L, L415T, and a combination thereof of SEQ ID NO: 6, optionally wherein the mutation is E210D, Q459L and L415T.
 21. (canceled)
 22. The genetically modified DXS enzyme according to claim 19, comprising an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to an amino acid sequence set forth in SEQ ID NO: 24 or SEQ ID NO:
 25. 23. A genetically modified fungal terpene synthase (FTPS), wherein the genetic modification is a mutation at one or more amino acid positions.
 24. The genetically modified FTPS according to claim 23, wherein the unmodified FTPS is isolated from Agrocybe aegerita or Agrocybe pediades, optionally wherein the mutation is an amino acid substitution, insertion, deletion, C-terminal truncation, N-terminal truncation, 1UP-3DW mutation, or 3UP-1DW mutation, optionally wherein wherein the mutation is selected from the group consisting of F204D, F204G, F204R, F204I, F204L, F204V, and combinations thereof of SEQ ID NO:
 3. 25.-26. (canceled)
 27. The genetically modified FTPS according to claim 23, comprising an amino acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to an amino acid sequence selected from the group consisting of: SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, and SEQ ID NO:23.
 28. A method of producing a terpenoid comprising a) culturing the bacterial strain according to claim 1 in an expression medium, or culturing a bacterial strain comprising a vector encoding a genetically modified FTPS wherein the genetic mutation is a mutation at one or more amino acid positions in an expression medium; and b) isolating the terpenoid from said expression medium.
 29. (canceled)
 30. The method according to claim 28, wherein the method further comprises the step of isolating the FTPS from the bacterial cell and mixing the isolated FTPS with one or more terpene precursors to produce the terpenoid, optionally wherein the isolated FTPS is further purified prior to mixing with one or more terpene precursors, optionally wherein the isolated FTPS is further mixed with one or more additional enzymes prior to mixing with one or more terpene precursors. 31.-32. (canceled)
 33. The method of claim 30, wherein the one or more additional enzymes is Acetyl-CoA acetyltransferase, Hydroxymethylglutaryl-CoA synthase (HMGS), Hydroxymethylglutaryl-CoA synthase reductase (HMGR), IDI, melonate kinase (MK), Phosphomevalonate kinase (PMK), mevalonate diphosphate decarboxylase (MVD1), or FPP synthase (ispA).
 34. The method according to claim 28, wherein the product is a monoterpenoid, sesquiterpenoid, or a mixture of both.
 35. (canceled) 